Psyllid ID: psy7053

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60-----
Protein Sequence
MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF
Secondary Structure (PSIPRED)
ccccccccccccccEEEEccccccccHHHHHHHHHccccEEEEEEcccccccccccEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEEEEEcccccccHHHHHHHHHHcccccEEEEcccccccccccEEEEEEEcc
Coil and Loop (DISEMBL)
msygrpppriegmvslkvdnltyrttpdDLRRVFERCgevgdiyiprdrftresrGFAFVRLLLF
Flexible Loop (DISEMBL)
msygrpppriegmvslkvdnltyrttpddlrrVFERcgevgdiyiprdrftresrgfAFVRLLLF
Low Complexity Region (SEG)
MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF
Disordered region (IsUnstruct)
*************VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL*
Disordered Region (DISOPRED)
****************KVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF
Disordered Region (DISEMBL)
MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF
Disordered Region (DISPRO)
****RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	65	2.2.26 [Sep-21-2011]
Q5R1W5	221	Serine/arginine-rich spli	yes	N/A	0.953	0.280	0.806	9e-24
P30352	221	Serine/arginine-rich spli	yes	N/A	0.953	0.280	0.806	1e-23
Q06A98	221	Serine/arginine-rich spli	yes	N/A	0.953	0.280	0.806	1e-23
Q6PDU1	221	Serine/arginine-rich spli	yes	N/A	0.953	0.280	0.806	1e-23
Q62093	221	Serine/arginine-rich spli	yes	N/A	0.953	0.280	0.806	1e-23
Q01130	221	Serine/arginine-rich spli	yes	N/A	0.953	0.280	0.806	1e-23
Q3MHR5	221	Serine/arginine-rich spli	yes	N/A	0.953	0.280	0.806	1e-23
Q9BRL6	282	Serine/arginine-rich spli	no	N/A	0.953	0.219	0.693	4e-19
Q09511	196	Probable splicing factor,	no	N/A	0.892	0.295	0.603	8e-17
Q8WXF0	261	Serine/arginine-rich spli	no	N/A	0.846	0.210	0.466	5e-06

>sp|Q5R1W5|SRSF2_PANTR Serine/arginine-rich splicing factor 2 OS=Pan troglodytes GN=SRSF2 PE=2 SV=3

 Score =  108 bits (270), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 50/62 (80%), Positives = 56/62 (90%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Binds to purine-rich RNA sequences, either 5'-AGSAGAGTA-3' (S=C or G) or 5'-GTTCGAGTA-3'. Can bind to beta-globin mRNA and commit it to the splicing pathway. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment.
Pan troglodytes (taxid: 9598)

>sp|P30352|SRSF2_CHICK Serine/arginine-rich splicing factor 2 OS=Gallus gallus GN=SRSF2 PE=2 SV=1

 Score =  108 bits (270), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 50/62 (80%), Positives = 56/62 (90%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA.

Gallus gallus (taxid: 9031)

>sp|Q06A98|SRSF2_PIG Serine/arginine-rich splicing factor 2 OS=Sus scrofa GN=SRSF2 PE=2 SV=1

 Score =  108 bits (270), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 50/62 (80%), Positives = 56/62 (90%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Binds to purine-rich RNA sequences, either 5'-AGSAGAGTA-3' (S=C or G) or 5'-GTTCGAGTA-3'. Can bind to beta-globin mRNA and commit it to the splicing pathway. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment.

Sus scrofa (taxid: 9823)

>sp|Q6PDU1|SRSF2_RAT Serine/arginine-rich splicing factor 2 OS=Rattus norvegicus GN=Srsf2 PE=1 SV=3

 Score =  108 bits (269), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 50/62 (80%), Positives = 56/62 (90%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment.

Rattus norvegicus (taxid: 10116)

>sp|Q62093|SRSF2_MOUSE Serine/arginine-rich splicing factor 2 OS=Mus musculus GN=Srsf2 PE=1 SV=4

 Score =  108 bits (269), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 50/62 (80%), Positives = 56/62 (90%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA (By similarity). Can bind to the myelin basic protein (MBP) gene MB3 regulatory region and increase transcription of the mbp promoter in cells derived from the CNS. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment.

Mus musculus (taxid: 10090)

>sp|Q01130|SRSF2_HUMAN Serine/arginine-rich splicing factor 2 OS=Homo sapiens GN=SRSF2 PE=1 SV=4

 Score =  108 bits (269), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 50/62 (80%), Positives = 56/62 (90%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Binds to purine-rich RNA sequences, either 5'-AGSAGAGTA-3' (S=C or G) or 5'-GTTCGAGTA-3'. Can bind to beta-globin mRNA and commit it to the splicing pathway. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment.

Homo sapiens (taxid: 9606)

>sp|Q3MHR5|SRSF2_BOVIN Serine/arginine-rich splicing factor 2 OS=Bos taurus GN=SRSF2 PE=2 SV=3

 Score =  108 bits (269), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 50/62 (80%), Positives = 56/62 (90%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 1  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Necessary for the splicing of pre-mRNA. It is required for formation of the earliest ATP-dependent splicing complex and interacts with spliceosomal components bound to both the 5'- and 3'-splice sites during spliceosome assembly. It also is required for ATP-dependent interactions of both U1 and U2 snRNPs with pre-mRNA. Interacts with other spliceosomal components, via the RS domains, to form a bridge between the 5'- and 3'-splice site binding components, U1 snRNP and U2AF. Binds to purine-rich RNA sequences, either 5'-AGSAGAGTA-3' (S=C or G) or 5'-GTTCGAGTA-3'. Can bind to beta-globin mRNA and commit it to the splicing pathway. The phosphorylated form (by SRPK2) is required for cellular apoptosis in response to cisplatin treatment.

Bos taurus (taxid: 9913)

>sp|Q9BRL6|SRSF8_HUMAN Serine/arginine-rich splicing factor 8 OS=Homo sapiens GN=SRSF8 PE=1 SV=1

 Score = 93.2 bits (230), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 43/62 (69%), Positives = 52/62 (83%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MS GRPPP ++GM++LKVDNLTYRT+PD LRRVFE+ G VGD+YIPR+  T+  RGFAFV
Sbjct: 1  MSCGRPPPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Involved in pre-mRNA alternative splicing.

Homo sapiens (taxid: 9606)

>sp|Q09511|RSP4_CAEEL Probable splicing factor, arginine/serine-rich 4 OS=Caenorhabditis elegans GN=rsp-4 PE=3 SV=1

 Score = 85.5 bits (210), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 35/58 (60%), Positives = 49/58 (84%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
          R  P I G+ SLK+DNL+Y+TTP+DLRR FER G++GD++IPRD+++R+S+GF FVR 
Sbjct: 10 RAAPDINGLTSLKIDNLSYQTTPNDLRRTFERYGDIGDVHIPRDKYSRQSKGFGFVRF 67

May play a functionally redundant role in embryogenesis.

Caenorhabditis elegans (taxid: 6239)

>sp|Q8WXF0|SRS12_HUMAN Serine/arginine-rich splicing factor 12 OS=Homo sapiens GN=SRSF12 PE=2 SV=1

 Score = 49.7 bits (117), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 28/60 (46%), Positives = 36/60 (60%), Gaps = 5/60 (8%)

Query: 3  YGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
          Y RPP       SL + N+   T P+DLRR F R G + D+YIP D +TR  RGFA+V+ 
Sbjct: 4  YTRPPN-----TSLFIRNVADATRPEDLRREFGRYGPIVDVYIPLDFYTRRPRGFAYVQF 58

Splicing factor that seems to antagonize SR proteins in pre-mRNA splicing regulation.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	65
332373880	168	unknown [Dendroctonus ponderosae]	0.953	0.369	0.983	3e-28
307169015	208	Splicing factor, arginine/serine-rich 2	0.938	0.293	0.967	3e-27
345486316	198	PREDICTED: serine/arginine-rich splicing	0.953	0.313	0.951	1e-26
240849499	153	serine/arginine rich splicing factor-lik	0.953	0.405	0.951	2e-26
322789593	175	hypothetical protein SINV_10987 [Solenop	0.953	0.354	0.951	2e-26
307197633	175	Splicing factor, arginine/serine-rich 2	0.953	0.354	0.951	2e-26
242005811	246	serine/arginine rich splicing factor, pu	0.953	0.252	0.919	2e-26
110762781	176	PREDICTED: serine/arginine-rich splicing	0.953	0.352	0.951	2e-26
357608819	165	putative serine/arginine rich splicing f	0.969	0.381	0.920	6e-26
114050755	154	Sr protein [Bombyx mori] gi|87248221|gb|	0.969	0.409	0.920	7e-26

>gi|332373880|gb|AEE62081.1| unknown [Dendroctonus ponderosae]

 Score =  128 bits (322), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 61/62 (98%), Positives = 61/62 (98%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307169015|gb|EFN61874.1| Splicing factor, arginine/serine-rich 2 [Camponotus floridanus]

 Score =  125 bits (315), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 59/61 (96%), Positives = 61/61 (100%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRI+GMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYGRPPPRIDGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 R 61
          R
Sbjct: 61 R 61

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345486316|ref|XP_003425445.1| PREDICTED: serine/arginine-rich splicing factor 2-like [Nasonia vitripennis]

 Score =  123 bits (309), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 59/62 (95%), Positives = 61/62 (98%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRI+GMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYGRPPPRIDGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|240849499|ref|NP_001155685.1| serine/arginine rich splicing factor-like [Acyrthosiphon pisum] gi|239790824|dbj|BAH71947.1| ACYPI006902 [Acyrthosiphon pisum]

 Score =  123 bits (308), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 59/62 (95%), Positives = 60/62 (96%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSY RPPPRIEGMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYSRPPPRIEGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322789593|gb|EFZ14819.1| hypothetical protein SINV_10987 [Solenopsis invicta] gi|332021256|gb|EGI61641.1| Splicing factor, arginine/serine-rich 2 [Acromyrmex echinatior]

 Score =  123 bits (308), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 59/62 (95%), Positives = 61/62 (98%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRI+GMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYGRPPPRIDGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307197633|gb|EFN78812.1| Splicing factor, arginine/serine-rich 2 [Harpegnathos saltator]

 Score =  123 bits (308), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 59/62 (95%), Positives = 61/62 (98%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRI+GMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYGRPPPRIDGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242005811|ref|XP_002423754.1| serine/arginine rich splicing factor, putative [Pediculus humanus corporis] gi|212506956|gb|EEB11016.1| serine/arginine rich splicing factor, putative [Pediculus humanus corporis]

 Score =  122 bits (307), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 57/62 (91%), Positives = 61/62 (98%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           +SYGRPPPRI+GMVSLKVDNLT+RTTPDDLRRVFERCGEVGDIYIPRDRF+RESRGFAFV
Sbjct: 48  VSYGRPPPRIDGMVSLKVDNLTFRTTPDDLRRVFERCGEVGDIYIPRDRFSRESRGFAFV 107

Query: 61  RL 62
           R 
Sbjct: 108 RF 109

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110762781|ref|XP_393352.2| PREDICTED: serine/arginine-rich splicing factor 2-like [Apis mellifera] gi|340724784|ref|XP_003400761.1| PREDICTED: serine/arginine-rich splicing factor 2-like [Bombus terrestris] gi|350398198|ref|XP_003485116.1| PREDICTED: serine/arginine-rich splicing factor 2-like [Bombus impatiens] gi|380022396|ref|XP_003695032.1| PREDICTED: serine/arginine-rich splicing factor 2-like [Apis florea] gi|383865619|ref|XP_003708270.1| PREDICTED: serine/arginine-rich splicing factor 2-like [Megachile rotundata]

 Score =  122 bits (307), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 59/62 (95%), Positives = 61/62 (98%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRI+GMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDRFTRESRGFAFV
Sbjct: 1  MSYGRPPPRIDGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60

Query: 61 RL 62
          R 
Sbjct: 61 RF 62

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357608819|gb|EHJ66166.1| putative serine/arginine rich splicing factor [Danaus plexippus]

 Score =  121 bits (303), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 58/63 (92%), Positives = 61/63 (96%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRI+GMVSLKVDNLTYRTTPDDLRRVFERCG+VGDIYIPRDR+TRESRGFAFV
Sbjct: 1  MSYGRPPPRIDGMVSLKVDNLTYRTTPDDLRRVFERCGDVGDIYIPRDRYTRESRGFAFV 60

Query: 61 RLL 63
          R  
Sbjct: 61 RFF 63

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|114050755|ref|NP_001040152.1| Sr protein [Bombyx mori] gi|87248221|gb|ABD36163.1| Sr protein [Bombyx mori]

 Score =  121 bits (303), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 58/63 (92%), Positives = 61/63 (96%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPPRI+GMVSLKVDNLTYRTTP+DLRRVFERCGEVGDIYIPRDR+TRESRGFAFV
Sbjct: 1  MSYGRPPPRIDGMVSLKVDNLTYRTTPEDLRRVFERCGEVGDIYIPRDRYTRESRGFAFV 60

Query: 61 RLL 63
          R  
Sbjct: 61 RFF 63

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	65
UNIPROTKB|P30352	221	SRSF2 "Serine/arginine-rich sp	0.938	0.276	0.819	4.2e-24
UNIPROTKB|Q3MHR5	221	SRSF2 "Serine/arginine-rich sp	0.938	0.276	0.819	4.2e-24
UNIPROTKB|E2RDB2	221	SRSF2 "Uncharacterized protein	0.938	0.276	0.819	4.2e-24
UNIPROTKB|B4DN89	209	SRSF2 "Serine/arginine-rich-sp	0.938	0.291	0.819	4.2e-24
UNIPROTKB|J3KP15	134	SRSF2 "Serine/arginine-rich-sp	0.938	0.455	0.819	4.2e-24
UNIPROTKB|J3QL05	130	SRSF2 "Serine/arginine-rich-sp	0.938	0.469	0.819	4.2e-24
UNIPROTKB|Q01130	221	SRSF2 "Serine/arginine-rich sp	0.938	0.276	0.819	4.2e-24
UNIPROTKB|Q06A98	221	SRSF2 "Serine/arginine-rich sp	0.938	0.276	0.819	4.2e-24
MGI|MGI:98284	221	Srsf2 "serine/arginine-rich sp	0.938	0.276	0.819	4.2e-24
RGD|1359422	221	Srsf2 "serine/arginine-rich sp	0.938	0.276	0.819	4.2e-24

UNIPROTKB|P30352 SRSF2 "Serine/arginine-rich splicing factor 2" [Gallus gallus (taxid:9031)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 50/61 (81%), Positives = 56/61 (91%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 R 61
             R
Sbjct:    61 R 61

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q3MHR5 SRSF2 "Serine/arginine-rich splicing factor 2" [Bos taurus (taxid:9913)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 50/61 (81%), Positives = 56/61 (91%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 R 61
             R
Sbjct:    61 R 61

GO:0016607 "nuclear speck" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2RDB2 SRSF2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 50/61 (81%), Positives = 56/61 (91%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 R 61
             R
Sbjct:    61 R 61

GO:0016607 "nuclear speck" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|B4DN89 SRSF2 "Serine/arginine-rich-splicing factor 2" [Homo sapiens (taxid:9606)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 50/61 (81%), Positives = 56/61 (91%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 R 61
             R
Sbjct:    61 R 61

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|J3KP15 SRSF2 "Serine/arginine-rich-splicing factor 2" [Homo sapiens (taxid:9606)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 50/61 (81%), Positives = 56/61 (91%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 R 61
             R
Sbjct:    61 R 61

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|J3QL05 SRSF2 "Serine/arginine-rich-splicing factor 2" [Homo sapiens (taxid:9606)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 50/61 (81%), Positives = 56/61 (91%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 R 61
             R
Sbjct:    61 R 61

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q01130 SRSF2 "Serine/arginine-rich splicing factor 2" [Homo sapiens (taxid:9606)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 50/61 (81%), Positives = 56/61 (91%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 R 61
             R
Sbjct:    61 R 61

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0016605 "PML body" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0003714 "transcription corepressor activity" evidence=NAS

GO:0016607 "nuclear speck" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0006397 "mRNA processing" evidence=TAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006406 "mRNA export from nucleus" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0031124 "mRNA 3'-end processing" evidence=TAS

UNIPROTKB|Q06A98 SRSF2 "Serine/arginine-rich splicing factor 2" [Sus scrofa (taxid:9823)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 50/61 (81%), Positives = 56/61 (91%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 R 61
             R
Sbjct:    61 R 61

GO:0016607 "nuclear speck" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:98284 Srsf2 "serine/arginine-rich splicing factor 2" [Mus musculus (taxid:10090)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 50/61 (81%), Positives = 56/61 (91%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 R 61
             R
Sbjct:    61 R 61

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=ISO;IDA

RGD|1359422 Srsf2 "serine/arginine-rich splicing factor 2" [Rattus norvegicus (taxid:10116)]

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 50/61 (81%), Positives = 56/61 (91%)

Query:     1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct:     1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 60

Query:    61 R 61
             R
Sbjct:    61 R 61

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=IEA;ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA;ISO

GO:0016605 "PML body" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q06A98	SRSF2_PIG	No assigned EC number	0.8064	0.9538	0.2805	yes	N/A
P30352	SRSF2_CHICK	No assigned EC number	0.8064	0.9538	0.2805	yes	N/A
Q01130	SRSF2_HUMAN	No assigned EC number	0.8064	0.9538	0.2805	yes	N/A
Q6PDU1	SRSF2_RAT	No assigned EC number	0.8064	0.9538	0.2805	yes	N/A
Q3MHR5	SRSF2_BOVIN	No assigned EC number	0.8064	0.9538	0.2805	yes	N/A
Q62093	SRSF2_MOUSE	No assigned EC number	0.8064	0.9538	0.2805	yes	N/A
Q5R1W5	SRSF2_PANTR	No assigned EC number	0.8064	0.9538	0.2805	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	65
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	4e-26
smart00360	73	smart00360, RRM, RNA recognition motif	2e-13
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	8e-12
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-11
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-10
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-10
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-10
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-10
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-10
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	7e-10
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-09
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-09
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-09
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-08
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-08
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	4e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	4e-08
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	5e-08
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	6e-08
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	8e-08
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	1e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-07
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-07
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-07
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	3e-07
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	5e-07
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-06
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-06
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-06
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	2e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	3e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	4e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-06
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	6e-06
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	8e-06
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	8e-06
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	1e-05
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	1e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	1e-05
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	1e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	1e-05
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	2e-05
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-05
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	2e-05
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	3e-05
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	4e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	7e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	8e-05
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	8e-05
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	9e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	9e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-04
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	1e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	1e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	2e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-04
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-04
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	2e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	3e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	3e-04
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	4e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	5e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	5e-04
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	6e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	6e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	7e-04
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	9e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	9e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.001
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	0.001
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	0.001
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	0.001
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.001
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	0.001
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	0.001
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	0.001
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	0.001
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	0.001
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	0.001
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.001
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.002
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	0.002
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	0.002
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	0.002
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.002
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	0.002
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	0.002
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.002
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.002
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	0.002
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	0.002
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	0.003
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	0.003
cd12396	85	cd12396, RRM1_Nop13p_fungi, RNA recognition motif	0.003

>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins

 Score = 90.0 bits (224), Expect = 4e-26
 Identities = 42/46 (91%), Positives = 45/46 (97%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          LKVDNLTYRTTPDDLRRVFE+ GEVGD+YIPRDR+TRESRGFAFVR
Sbjct: 1  LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVR 46

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 58.0 bits (141), Expect = 2e-13
 Identities = 20/47 (42%), Positives = 31/47 (65%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          +L V NL   TT ++LR +F + G+V  + + RD+ T +S+GFAFV 
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVE 47

Length = 73

>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins

 Score = 54.3 bits (131), Expect = 8e-12
 Identities = 25/46 (54%), Positives = 32/46 (69%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          SL V N+   T PDDLRR+F + G + D+YIP D +TR  RGFA+V
Sbjct: 2  SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYV 47

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 53.3 bits (129), Expect = 1e-11
 Identities = 19/46 (41%), Positives = 30/46 (65%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +++V NL+     DDLR +F   G +  +Y+ +D+ T +SRGFAFV
Sbjct: 1  TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFV 46

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 53.0 bits (128), Expect = 2e-11
 Identities = 19/45 (42%), Positives = 27/45 (60%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V  L+ RTT  +L  +F + G V ++ + +D  T ESRGF FV
Sbjct: 4  LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFV 48

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 51.1 bits (123), Expect = 1e-10
 Identities = 21/46 (45%), Positives = 27/46 (58%), Gaps = 1/46 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          L V NL   TT +DL+ +F + G +  I I RD  T  S+GFAFV 
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVE 45

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 51.1 bits (123), Expect = 1e-10
 Identities = 21/45 (46%), Positives = 26/45 (57%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V NL Y  T +DL+ +F + GEV    +  DR T  SRGF FV
Sbjct: 2  LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFV 46

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 50.0 bits (120), Expect = 2e-10
 Identities = 19/46 (41%), Positives = 31/46 (67%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          S+ V N+ Y TTP++L+  F+ CG +  I I  D+FT + +GFA++
Sbjct: 1  SIFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYI 46

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 50.0 bits (120), Expect = 3e-10
 Identities = 21/46 (45%), Positives = 33/46 (71%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          L V NL + TT ++LR +FE  GE+ ++++P D+ T+ S+GFAFV 
Sbjct: 2  LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVS 47

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 50.1 bits (120), Expect = 4e-10
 Identities = 18/48 (37%), Positives = 31/48 (64%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL 63
          L V NL Y    DDL ++F + GE+ ++++  D+ + +S+GFA+V  L
Sbjct: 5  LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFL 52

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 49.6 bits (119), Expect = 4e-10
 Identities = 21/46 (45%), Positives = 29/46 (63%), Gaps = 1/46 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          L V NL   TT +DLR +F + GE+  + I RD+   +S+GFAFV 
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVE 45

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 49.2 bits (118), Expect = 7e-10
 Identities = 19/43 (44%), Positives = 26/43 (60%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L Y TT D LR+ F + GE+ +  +  DR T +SRG+ FV
Sbjct: 5  VGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFV 47

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 48.9 bits (117), Expect = 1e-09
 Identities = 17/46 (36%), Positives = 31/46 (67%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          ++ V NL +  T +DL ++F + G+V  + I +D+ TR+S+G AF+
Sbjct: 3  TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFI 48

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 48.4 bits (116), Expect = 1e-09
 Identities = 20/46 (43%), Positives = 28/46 (60%), Gaps = 3/46 (6%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESR---GFAFV 60
          V NL ++   DDLR +F + GEV  I IP+ +  ++ R   GFAFV
Sbjct: 5  VRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFV 50

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 47.8 bits (114), Expect = 2e-09
 Identities = 18/46 (39%), Positives = 27/46 (58%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          L V  L ++TT  DL+  F   GE+  + + +D  T +S+GF FVR
Sbjct: 2  LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVR 47

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 47.8 bits (114), Expect = 2e-09
 Identities = 17/49 (34%), Positives = 33/49 (67%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL 64
          L + NL Y  T +DL ++F + G + ++++P D+ T++ +GFAFV  ++
Sbjct: 5  LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMI 53

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 47.3 bits (113), Expect = 3e-09
 Identities = 19/45 (42%), Positives = 27/45 (60%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V NL +  T DDLR +FE  GE+  + + RD  T  S+G+ F+
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFI 45

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 49.9 bits (118), Expect = 5e-09
 Identities = 23/47 (48%), Positives = 31/47 (65%)

Query: 15  SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           +L V NL Y  T +DLR +F++ G V  + + RDR T +SRGFAFV 
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVE 163

Length = 306

>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 45.7 bits (109), Expect = 1e-08
 Identities = 19/40 (47%), Positives = 24/40 (60%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L++ TT + LR  F + GEV D  I +D  T  SRGF FV
Sbjct: 6  LSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFV 45

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 45.8 bits (108), Expect = 2e-08
 Identities = 23/47 (48%), Positives = 32/47 (68%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          SL V N+   T P+DLRR F R G + D+Y+P D +TR  RGFA+++
Sbjct: 2  SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQ 48

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 45.0 bits (106), Expect = 4e-08
 Identities = 23/48 (47%), Positives = 31/48 (64%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
          SL V N+   T  +DLRR F R G + D+Y+P D +TR  RGFA+V+ 
Sbjct: 2  SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQF 49

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 44.6 bits (106), Expect = 4e-08
 Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V NL ++ T  DL+++F   G V ++ IPR    +  +GFAFV
Sbjct: 2  LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGK-KKGFAFV 45

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 44.3 bits (105), Expect = 5e-08
 Identities = 17/40 (42%), Positives = 26/40 (65%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L+++TT + LR  F + GE+ +  + RD  T+ SRGF FV
Sbjct: 6  LSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFV 45

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 44.3 bits (105), Expect = 6e-08
 Identities = 15/43 (34%), Positives = 25/43 (58%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V+ L    T + L+ VF + G V  + +PR + T + +GFAF+
Sbjct: 4  VECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFI 46

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 44.2 bits (105), Expect = 8e-08
 Identities = 18/45 (40%), Positives = 28/45 (62%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          + +  L Y  T  D+  VF + GE+ DI + RD+ T +S+GFAF+
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFL 56

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 43.4 bits (103), Expect = 1e-07
 Identities = 20/43 (46%), Positives = 25/43 (58%), Gaps = 5/43 (11%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  LT   T +DLR+ F + GEV D+YIP+       R FAFV
Sbjct: 5  VGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFV 42

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 43.5 bits (103), Expect = 1e-07
 Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V NL++    DDL   F+ CGEV D+ I +D   R S+GF  V
Sbjct: 4  VGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGR-SKGFGHV 45

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 43.7 bits (104), Expect = 1e-07
 Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 2/45 (4%)

Query: 20 NLTYRTTPDDLRRVFERCGEVG--DIYIPRDRFTRESRGFAFVRL 62
           L   TT +D+ +       V   D+ + RD+ T  SRGFAFV  
Sbjct: 9  GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEF 53

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 43.4 bits (103), Expect = 1e-07
 Identities = 20/45 (44%), Positives = 25/45 (55%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V  L+  TT  DLR VF R G +  + +  D+ T  SRGF FV
Sbjct: 2  LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFV 46

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 42.7 bits (101), Expect = 2e-07
 Identities = 18/40 (45%), Positives = 25/40 (62%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L+Y TT D L+  F + GE+ D  + +D  T+ SRGF FV
Sbjct: 7  LSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFV 46

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 43.0 bits (102), Expect = 2e-07
 Identities = 20/45 (44%), Positives = 26/45 (57%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V  L Y TT   LRR FE  G +  I + RD+ T + RG+AF+
Sbjct: 4  LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFI 48

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 42.2 bits (100), Expect = 3e-07
 Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 2/47 (4%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
          L V NL    T +DLR  F   G+V  + + R+      RGFAFV  
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEF 45

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 42.3 bits (100), Expect = 3e-07
 Identities = 16/43 (37%), Positives = 29/43 (67%), Gaps = 1/43 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V NL Y    D+LR++F +CGE+ D+ + ++   + S+G+A+V
Sbjct: 4  VSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGK-SKGYAYV 45

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 42.5 bits (100), Expect = 3e-07
 Identities = 21/44 (47%), Positives = 28/44 (63%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          V  L++ TT + LRR F + GEV D  I +D+ T  SRGF FV+
Sbjct: 4  VGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVK 47

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 41.8 bits (99), Expect = 5e-07
 Identities = 15/36 (41%), Positives = 25/36 (69%)

Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          T +D+R +FE  G + ++ I RD+ T +S+G AFV+
Sbjct: 12 TEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVK 47

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 41.0 bits (97), Expect = 1e-06
 Identities = 17/45 (37%), Positives = 23/45 (51%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V  LT     D L+ +F   G V D+ +P DR     RG+A+V
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYV 45

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 40.6 bits (96), Expect = 1e-06
 Identities = 18/43 (41%), Positives = 26/43 (60%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V NL +    ++LR+ FE CG+V  + I RDR T   +GF +V
Sbjct: 4  VGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYV 46

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 40.8 bits (96), Expect = 1e-06
 Identities = 18/45 (40%), Positives = 25/45 (55%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V+ L    T ++LR +FE  G +    I RDR T +S G+ FV
Sbjct: 3  LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFV 47

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 40.4 bits (94), Expect = 2e-06
 Identities = 18/43 (41%), Positives = 28/43 (65%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +  L+++T+PD LR  F + GE+ +  + RD  T+ SRGF FV
Sbjct: 4  IGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFV 46

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 39.9 bits (94), Expect = 3e-06
 Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 6/44 (13%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          V NL +  T ++L+R F   G + ++ + +D      +G+AFVR
Sbjct: 5  VGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVR 42

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 39.9 bits (94), Expect = 3e-06
 Identities = 17/46 (36%), Positives = 28/46 (60%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL 63
          V NL  + T + L  +F + G V +++IP+DR T+  +G+ FV  L
Sbjct: 3  VGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFL 48

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 41.8 bits (98), Expect = 3e-06
 Identities = 20/54 (37%), Positives = 31/54 (57%)

Query: 7   PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           P  I   + L V NL +  T  +LR++FE  G++ D+ + RD  T  S+GF F+
Sbjct: 180 PGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFI 233

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 39.6 bits (93), Expect = 4e-06
 Identities = 17/37 (45%), Positives = 26/37 (70%)

Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           T DDLR  F   GE+ DI++ +D+ T+ES+G A+V+
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVK 50

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins

 Score = 39.4 bits (93), Expect = 4e-06
 Identities = 18/46 (39%), Positives = 23/46 (50%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          SL V +L    T   L  +F   G V  I + RD  TR S G+A+V
Sbjct: 1  SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYV 46

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 39.1 bits (92), Expect = 4e-06
 Identities = 17/43 (39%), Positives = 25/43 (58%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L+ +    DL   F + G+V D+ I RDR +R S+G A+V
Sbjct: 4  VMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYV 46

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 39.1 bits (92), Expect = 6e-06
 Identities = 18/43 (41%), Positives = 27/43 (62%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V NL++ TT + +  +F RCG++  I +  DRFT+   GF FV
Sbjct: 3  VGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFV 45

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 39.1 bits (91), Expect = 8e-06
 Identities = 16/46 (34%), Positives = 28/46 (60%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          L +  L++ T    L +VF + G++ ++ + +DR T+ SRGF FV 
Sbjct: 3  LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 48

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 39.2 bits (91), Expect = 8e-06
 Identities = 22/45 (48%), Positives = 28/45 (62%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 56

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 38.5 bits (89), Expect = 1e-05
 Identities = 20/45 (44%), Positives = 27/45 (60%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L +  L++ TT D LR  FE+ G + D  + RD  T+ SRGF FV
Sbjct: 5  LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFV 49

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 38.3 bits (89), Expect = 1e-05
 Identities = 19/40 (47%), Positives = 23/40 (57%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L + TT D LR  F + GEV D  + RD  T  SRGF F+
Sbjct: 6  LNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFL 45

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 38.0 bits (89), Expect = 1e-05
 Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 6/47 (12%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
          L V NL    T ++ + +F + GEV ++++ ++      +GF F+RL
Sbjct: 4  LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRL 44

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 38.1 bits (89), Expect = 1e-05
 Identities = 17/43 (39%), Positives = 24/43 (55%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V NL Y TT +DL   F+  G    + +  D+ T +S+G AFV
Sbjct: 5  VGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFV 47

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 38.1 bits (88), Expect = 1e-05
 Identities = 18/46 (39%), Positives = 28/46 (60%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL 63
          +  L+++TT + LR  F + GEV +  + RD  T+ SRGF FV  +
Sbjct: 5  IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 50

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 38.1 bits (89), Expect = 1e-05
 Identities = 14/33 (42%), Positives = 19/33 (57%)

Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
            L   F  CGE+  + IP DR T  S+GFA++
Sbjct: 18 RSLTEHFSSCGEITRVSIPTDRETGASKGFAYI 50

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 37.9 bits (88), Expect = 2e-05
 Identities = 14/46 (30%), Positives = 27/46 (58%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          S+ V N+ Y +T ++L   F  CG +  + I  D+F+   +G+A++
Sbjct: 1  SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYI 46

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 38.0 bits (89), Expect = 2e-05
 Identities = 20/45 (44%), Positives = 25/45 (55%), Gaps = 1/45 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L+V NL Y  T +DL  +F R GEV  + I  DR +  S G A V
Sbjct: 3  LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADV 46

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 37.8 bits (88), Expect = 2e-05
 Identities = 17/45 (37%), Positives = 24/45 (53%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V NL++    + L+  FE+ G V    +  DR T  SRGF +V
Sbjct: 2  LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYV 46

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 37.5 bits (87), Expect = 2e-05
 Identities = 17/46 (36%), Positives = 25/46 (54%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           L V  L  +T+   LRR F R G++ +  +  D  T+ SRGF F+
Sbjct: 4  KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFI 49

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 37.3 bits (87), Expect = 3e-05
 Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFV 60
          L V NLT+ TT +DL       G  +V  I     +   +S+GFA+V
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYV 47

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 37.2 bits (86), Expect = 4e-05
 Identities = 20/43 (46%), Positives = 24/43 (55%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L++ TT  DL+  F + GEV D  I  D  T  SRGF FV
Sbjct: 3  VGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFV 45

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 36.5 bits (84), Expect = 7e-05
 Identities = 18/43 (41%), Positives = 24/43 (55%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +  L++ TT  DL+  F + GEV D  +  D  T  SRGF FV
Sbjct: 3  IGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFV 45

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 36.2 bits (83), Expect = 8e-05
 Identities = 19/45 (42%), Positives = 27/45 (60%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV
Sbjct: 5  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 49

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 36.1 bits (84), Expect = 8e-05
 Identities = 16/36 (44%), Positives = 21/36 (58%)

Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           T +DLR  F + G V  + I  D+ T + RGFAFV
Sbjct: 11 VTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFV 46

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 36.1 bits (83), Expect = 9e-05
 Identities = 17/43 (39%), Positives = 26/43 (60%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L+  TT +D+++ FE+ G+V D  +  D+ T   RGF FV
Sbjct: 4  VGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFV 46

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 36.1 bits (84), Expect = 9e-05
 Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 1/45 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V N+ +  T  +LR +F   G+V  + +P+ +F    RGFAFV
Sbjct: 3  LIVRNVPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFV 46

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 36.1 bits (84), Expect = 1e-04
 Identities = 13/43 (30%), Positives = 20/43 (46%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V N+ Y  T + L  +F   G V    +  DR T + +G+ F 
Sbjct: 3  VGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFC 45

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 36.0 bits (83), Expect = 1e-04
 Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          L V  L  + T  ++  VF   G V DIY+ RD   ++SRG AFV+
Sbjct: 2  LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVK 46

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 35.8 bits (83), Expect = 1e-04
 Identities = 15/43 (34%), Positives = 25/43 (58%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L+  TT + +R  F + G + +I +P D+ T + RGF F+
Sbjct: 4  VGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFI 46

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 35.9 bits (83), Expect = 1e-04
 Identities = 16/46 (34%), Positives = 26/46 (56%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          S+ V N+ Y  T ++L   F  CG V  + I  D+F+   +GFA++
Sbjct: 1  SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYI 46

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 35.9 bits (82), Expect = 1e-04
 Identities = 17/45 (37%), Positives = 28/45 (62%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L +  L++ TT + LR  +E+ G++ D  + RD  ++ SRGF FV
Sbjct: 5  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFV 49

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 36.9 bits (85), Expect = 2e-04
 Identities = 23/61 (37%), Positives = 30/61 (49%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           +SY RP        +L V NL    T D L  +F + G++    I RD+ T   RG AFV
Sbjct: 181 VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFV 240

Query: 61  R 61
           R
Sbjct: 241 R 241

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 35.4 bits (82), Expect = 2e-04
 Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          + NL +  T DD+R  F+ C E+  + +  D+ T E +GF  V
Sbjct: 4  IGNLAWDITEDDVREFFKGC-EITSVRLATDKETGEFKGFGHV 45

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 35.6 bits (82), Expect = 2e-04
 Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL 64
          V NL +  T  D+R +F   G++  + +P+ +F + +RGFAFV    
Sbjct: 5  VKNLPFEATKKDVRTLFSSYGQLKSVRVPK-KFDQSARGFAFVEFST 50

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 35.1 bits (81), Expect = 2e-04
 Identities = 17/43 (39%), Positives = 25/43 (58%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L+  TT DD+++ F + G+V D  +  D+ T   RGF FV
Sbjct: 4  VGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFV 46

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 35.2 bits (81), Expect = 2e-04
 Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 6/47 (12%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
          L V NL    T +++R++FE+ G+ G+I+I +D      +GF F+RL
Sbjct: 4  LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRL 44

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 35.1 bits (81), Expect = 2e-04
 Identities = 14/38 (36%), Positives = 24/38 (63%)

Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL 63
          T +DLR  F+  G++  + I +D+ T ES+GF +V+  
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFH 50

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 34.9 bits (81), Expect = 2e-04
 Identities = 13/36 (36%), Positives = 22/36 (61%)

Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          TT +DL  +F R G++    + RD+ T +S  +AF+
Sbjct: 15 TTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFI 50

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 34.9 bits (80), Expect = 2e-04
 Identities = 17/44 (38%), Positives = 25/44 (56%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          V NL +    + L RVF +CG +  + I RD  T   +GFA+V+
Sbjct: 4  VGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQ 47

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 34.9 bits (81), Expect = 2e-04
 Identities = 14/46 (30%), Positives = 23/46 (50%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +L + +L        +   F  CGEV  + I R++ T +S G+ FV
Sbjct: 1  TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFV 46

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins

 Score = 34.9 bits (81), Expect = 3e-04
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 5/51 (9%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-----FTRESRGFAFV 60
          +L V NL ++TT + L++ FE+CG V  + I + +         S G+ FV
Sbjct: 2  TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFV 52

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 35.3 bits (82), Expect = 3e-04
 Identities = 19/46 (41%), Positives = 29/46 (63%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +L V  L+ +TT + LR VF R G++  + + RD  T  S+G+AFV
Sbjct: 5  TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFV 50

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 35.0 bits (80), Expect = 3e-04
 Identities = 18/43 (41%), Positives = 24/43 (55%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L++ T+  DL+  F + GEV D  I  D  T  SRGF F+
Sbjct: 4  VGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFI 46

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 34.7 bits (80), Expect = 3e-04
 Identities = 16/45 (35%), Positives = 25/45 (55%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V+ L    T D++R +F   GE+    + RD+ T +S G+ FV
Sbjct: 4  LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFV 48

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 36.3 bits (84), Expect = 3e-04
 Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 14  VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           V+L V NL    T + LR +F  CGE+    +  D     SRGF FV
Sbjct: 286 VNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFV 331

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 34.5 bits (79), Expect = 4e-04
 Identities = 20/47 (42%), Positives = 28/47 (59%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          +L V NL  + T D+LR++FE  G +    + RD+ T   RG AFVR
Sbjct: 2  NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVR 48

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 34.2 bits (79), Expect = 5e-04
 Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  +   TT ++LR  F R G V D+ I  DR    S+G+ FV
Sbjct: 7  VGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFV 48

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 34.2 bits (78), Expect = 5e-04
 Identities = 17/43 (39%), Positives = 24/43 (55%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L+  TT + ++  F   GE+ +I +P D  T E RGF FV
Sbjct: 4  VGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFV 46

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 34.3 bits (78), Expect = 6e-04
 Identities = 16/43 (37%), Positives = 25/43 (58%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L+  T  +D+++ FE+ G+V D  +  D+ T   RGF FV
Sbjct: 8  VGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFV 50

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 33.9 bits (78), Expect = 6e-04
 Identities = 13/36 (36%), Positives = 20/36 (55%)

Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           T ++ +  F + G+V D  + +D  T  SRGF FV
Sbjct: 11 VTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFV 46

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 33.7 bits (78), Expect = 7e-04
 Identities = 14/43 (32%), Positives = 24/43 (55%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V NL Y TT + L   F   G +   ++ +D+ +++ RGF +V
Sbjct: 4  VRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYV 46

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 33.4 bits (77), Expect = 9e-04
 Identities = 12/34 (35%), Positives = 21/34 (61%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRD 48
          ++KV NL   TT + +R+ F+ CGE+ ++ I   
Sbjct: 2  TVKVKNLPKDTTENKIRQFFKDCGEIREVKIVES 35

This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 33.6 bits (77), Expect = 9e-04
 Identities = 16/43 (37%), Positives = 25/43 (58%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V NL++ TT D+LR  F R G +  + +     + + +GFAFV
Sbjct: 3  VGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFV 45

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 34.5 bits (79), Expect = 0.001
 Identities = 15/43 (34%), Positives = 23/43 (53%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           V  L  +    DL   F + G+V D+   +DR +R S+G A+V
Sbjct: 94  VLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYV 136

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 33.7 bits (78), Expect = 0.001
 Identities = 16/44 (36%), Positives = 27/44 (61%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          + NL +  T ++L+ +F + GEV    I +D+ T  S+G AFV+
Sbjct: 5  IRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVK 48

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 33.4 bits (76), Expect = 0.001
 Identities = 21/45 (46%), Positives = 26/45 (57%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V  L+  TT  DLR VF R G +  + +  D+ T  SRGFAFV
Sbjct: 2  LGVFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFV 46

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 33.4 bits (77), Expect = 0.001
 Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 5/45 (11%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V N+      ++LR +FE+ G++  +Y        + RGF  V
Sbjct: 4  LFVRNINSNVEDEELRALFEQFGDIRTLY-----TACKHRGFIMV 43

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 33.4 bits (77), Expect = 0.001
 Identities = 14/45 (31%), Positives = 20/45 (44%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V NL    T +  R +    G V   ++     T ES+G+ FV
Sbjct: 2  LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFV 46

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 33.5 bits (77), Expect = 0.001
 Identities = 11/33 (33%), Positives = 23/33 (69%)

Query: 28 DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           DLR +FE+ G++ ++ + +D++T   +G AF+
Sbjct: 20 KDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFL 52

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 33.3 bits (77), Expect = 0.001
 Identities = 18/45 (40%), Positives = 22/45 (48%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V  L        L   F   G++ DI IP D  T++ RGFAFV
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFV 45

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 33.1 bits (75), Expect = 0.001
 Identities = 13/43 (30%), Positives = 25/43 (58%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V +L+   T +D++  F   G++ D  + +D  T +S+G+ FV
Sbjct: 6  VGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFV 48

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 33.0 bits (75), Expect = 0.001
 Identities = 18/43 (41%), Positives = 22/43 (51%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +  L++ T+  DL     R GEV D  I  D  T  SRGF FV
Sbjct: 4  IGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFV 46

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 33.3 bits (76), Expect = 0.001
 Identities = 16/47 (34%), Positives = 22/47 (46%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          +L V NL +  T +DL   F     +    +  D  T ESRG+ FV 
Sbjct: 1  TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVT 47

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 33.1 bits (76), Expect = 0.001
 Identities = 16/33 (48%), Positives = 20/33 (60%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPR 47
          +L + NL   TT  DLR  FER GE+ DI I +
Sbjct: 4  TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKK 36

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 32.9 bits (76), Expect = 0.001
 Identities = 12/35 (34%), Positives = 21/35 (60%)

Query: 27 PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
            +LR+ F + G V  + + R + T +S+G+AFV 
Sbjct: 13 EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVE 47

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 33.9 bits (77), Expect = 0.002
 Identities = 18/45 (40%), Positives = 23/45 (51%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L +  L++ T    LR  F   G+V D  +  DR T  SRGF FV
Sbjct: 37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFV 81

Length = 144

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 32.6 bits (74), Expect = 0.002
 Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 6/47 (12%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
          L V NL    T +D +++FE+ GE  +++I RD      RGF F+RL
Sbjct: 4  LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRL 44

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 33.1 bits (75), Expect = 0.002
 Identities = 17/43 (39%), Positives = 22/43 (51%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL 63
          L  R  P DL   F   G+V D+ I  DR +R S+G A+V   
Sbjct: 9  LAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFC 51

This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In contrast to RBM39, RBM23 contains only two RRMs. . Length = 85

>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 32.7 bits (74), Expect = 0.002
 Identities = 16/43 (37%), Positives = 23/43 (53%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL 63
          L  R  P DL   F   G+V D+ +  DR +R S+G A+V  +
Sbjct: 9  LAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFV 51

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 32.8 bits (75), Expect = 0.002
 Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL 63
          +L V NL    T ++LRR FER G V D+ I R    + +  +AFV+ L
Sbjct: 4  TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGN-AYAFVKFL 51

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 32.7 bits (75), Expect = 0.002
 Identities = 12/35 (34%), Positives = 19/35 (54%)

Query: 26 TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          T  DLR+ F + G V ++ +  D   +  RGF F+
Sbjct: 15 TETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFI 49

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 32.5 bits (74), Expect = 0.002
 Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 4/46 (8%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +L V NL Y  T D+L+ VFE   +  DI +P  +    S+G A++
Sbjct: 5  TLFVKNLPYNITVDELKEVFE---DAVDIRLPSGK-DGSSKGIAYI 46

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 32.3 bits (74), Expect = 0.002
 Identities = 14/43 (32%), Positives = 23/43 (53%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V +L+     + LR  F   GE+ D  + +D  T +S+G+ FV
Sbjct: 4  VGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFV 46

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 32.3 bits (74), Expect = 0.002
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +L V NL  R T + L  +F + G +  + IP+D   +  + FAFV
Sbjct: 3  TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGK-PKSFAFV 47

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 32.6 bits (75), Expect = 0.002
 Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 16 LKVDNLTYRTTPDDLRRVFERC-GEVGDIYIPRDRFTRESRGFAFV 60
          L V NL    T  +L+  F +  GE+ D+ + R    + SR  AF+
Sbjct: 3  LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGK-SRRIAFI 47

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 32.5 bits (75), Expect = 0.002
 Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V NL      + L+ +F + G++    + +D    +S+GF FV
Sbjct: 6  VKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFV 47

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 32.3 bits (74), Expect = 0.003
 Identities = 13/45 (28%), Positives = 22/45 (48%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V NL++    D +   F   GE+  + +P D  +   +GF +V
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYV 45

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin

 Score = 32.2 bits (73), Expect = 0.003
 Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 5/45 (11%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V+NL+Y  + D L+ VFE+      I IP++      +G+AFV
Sbjct: 4  LVVNNLSYSASEDSLQEVFEK---ATSIRIPQNN--GRPKGYAFV 43

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 32.1 bits (73), Expect = 0.003
 Identities = 13/54 (24%), Positives = 28/54 (51%), Gaps = 11/54 (20%)

Query: 18 VDNLTYRTTPDDLRRVFER-------CGEVGDIYIPRDRFTR----ESRGFAFV 60
          + NL++ TT + LR+ F           ++  +++P  +  R    +++GFA+V
Sbjct: 3  IGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYV 56

This subfamily corresponds to the RRM1 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 85

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	65
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.68
KOG0149|consensus	247		99.65
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.63
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.62
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.6
KOG4207|consensus	256		99.58
KOG0113|consensus	335		99.55
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.54
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.53
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.53
KOG0126|consensus	219		99.51
KOG0122|consensus	270		99.51
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.5
KOG0121|consensus	153		99.49
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.46
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.46
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.45
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.44
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.43
PLN03120	260	nucleic acid binding protein; Provisional	99.42
PLN03213	759	repressor of silencing 3; Provisional	99.39
KOG0117|consensus	506		99.37
PLN03121	243	nucleic acid binding protein; Provisional	99.36
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.36
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.35
KOG0131|consensus	203		99.35
KOG0124|consensus	544		99.33
KOG0145|consensus	360		99.33
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.32
KOG0144|consensus	510		99.32
KOG0111|consensus	298		99.3
KOG0130|consensus	170		99.29
KOG0125|consensus	376		99.29
KOG4205|consensus	311		99.27
smart00362	72	RRM_2 RNA recognition motif.	99.26
KOG0127|consensus	678		99.26
KOG0148|consensus	321		99.25
KOG0108|consensus	435		99.22
smart00360	71	RRM RNA recognition motif.	99.21
KOG0107|consensus	195		99.21
KOG0124|consensus	544		99.18
KOG0144|consensus	510		99.16
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.14
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.11
KOG0148|consensus	321		99.08
KOG0114|consensus	124		99.08
KOG0105|consensus	241		99.07
KOG0127|consensus	678		99.03
KOG0146|consensus	371		99.02
KOG0147|consensus	549		99.02
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.01
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.96
KOG4208|consensus	214		98.96
KOG0146|consensus	371		98.94
KOG0145|consensus	360		98.93
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.9
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.88
KOG0131|consensus	203		98.86
KOG4205|consensus	311		98.81
KOG0415|consensus	479		98.79
KOG0110|consensus	725		98.74
KOG4212|consensus	608		98.74
KOG0123|consensus	369		98.72
KOG0117|consensus	506		98.7
KOG0116|consensus	419		98.68
smart00361	70	RRM_1 RNA recognition motif.	98.65
KOG0109|consensus	346		98.65
KOG4209|consensus	231		98.57
KOG0123|consensus	369		98.51
KOG4206|consensus	221		98.47
KOG0226|consensus	290		98.45
KOG0153|consensus	377		98.36
KOG0132|consensus	894		98.3
KOG0106|consensus	216		98.26
KOG4454|consensus	267		98.21
KOG4212|consensus	608		98.2
KOG0533|consensus	243		98.14
KOG4661|consensus	940		98.11
KOG0120|consensus	500		98.08
KOG4849|consensus	498		98.03
KOG0110|consensus	725		98.02
KOG4211|consensus	510		97.99
KOG0109|consensus	346		97.93
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	97.92
KOG4660|consensus	549		97.88
KOG0129|consensus	520		97.79
KOG4210|consensus	285		97.73
KOG1548|consensus	382		97.73
KOG4211|consensus	510		97.72
KOG0151|consensus	877		97.63
KOG0129|consensus	520		97.63
KOG0147|consensus	549		97.57
KOG1457|consensus	284		97.57
KOG1457|consensus	284		97.27
KOG1995|consensus	351		96.94
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.94
KOG1190|consensus	492		96.9
KOG4206|consensus	221		96.87
KOG0128|consensus	881		96.78
KOG3152|consensus	278		96.44
KOG0105|consensus	241		96.35
KOG0128|consensus	881		96.31
KOG0115|consensus	275		95.57
KOG2314|consensus	698		95.49
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	95.23
KOG4676|consensus	479		94.44
KOG4307|consensus	944		94.29
KOG4660|consensus	549		94.14
KOG1365|consensus	508		94.14
KOG4307|consensus	944		94.08
KOG1365|consensus	508		94.01
KOG1855|consensus	484		93.67
KOG4410|consensus	396		92.5
KOG0112|consensus	975		92.15
KOG0106|consensus	216		91.15
KOG2416|consensus	718		90.84
KOG1456|consensus	494		90.26
KOG0112|consensus	975		90.15
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	89.56
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	87.91
KOG1190|consensus	492		87.15
COG5175	480	MOT2 Transcriptional repressor [Transcription]	85.27
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	84.78
KOG2193|consensus	584		84.55
KOG4210|consensus	285		84.04

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.68  E-value=4.1e-16  Score=82.10  Aligned_cols=54  Identities=33%  Similarity=0.411  Sum_probs=50.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+.+++++|+++|.+||.|.++.++.++.+++++|||||+|.+
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~   85 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFND   85 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECC
Confidence            445789999999999999999999999999999999999999999999999986

>KOG0149|consensus

Probab=99.65  E-value=4.6e-16  Score=86.36  Aligned_cols=51  Identities=31%  Similarity=0.529  Sum_probs=49.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+||||+|+|.+..+.|++.|++||+|.+..++.|+.+|++||||||.|..
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d   63 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRD   63 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeec
Confidence            689999999999999999999999999999999999999999999999975

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.63  E-value=4.4e-15  Score=86.35  Aligned_cols=54  Identities=28%  Similarity=0.355  Sum_probs=50.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+.+|||+|||+.+++++|.++|++||.|.+++++.++.++.++|||||+|.+
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~  320 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTN  320 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECC
Confidence            344579999999999999999999999999999999999999999999999986

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.62  E-value=6e-15  Score=86.51  Aligned_cols=56  Identities=29%  Similarity=0.282  Sum_probs=51.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||++||+++++++|+++|..+|.|.+++++.+..+++++|||||+|.+
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~  158 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGS  158 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEcc
Confidence            34456899999999999999999999999999999999999999999999999976

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.60  E-value=6.6e-15  Score=85.61  Aligned_cols=53  Identities=28%  Similarity=0.496  Sum_probs=50.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+|||+|||..+++++|+++|..+|.|.+++++.++.+|+++|||||+|.+
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~   54 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVR   54 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECc
Confidence            34799999999999999999999999999999999999899999999999975

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG4207|consensus

Probab=99.58  E-value=1e-14  Score=80.22  Aligned_cols=64  Identities=80%  Similarity=1.368  Sum_probs=61.7

Q ss_pred             CCCCCCCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         1 ~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |+++.+|++.+....|-|-||.+-++.++|+.+|++||.|.+++++.|+-|++++|||||.|..
T Consensus         1 MS~g~~PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~   64 (256)
T KOG4207|consen    1 MSYGRPPPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHD   64 (256)
T ss_pred             CCCCCCCCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeee
Confidence            8999999999999999999999999999999999999999999999999999999999999963

>KOG0113|consensus

Probab=99.55  E-value=3e-14  Score=81.50  Aligned_cols=53  Identities=36%  Similarity=0.589  Sum_probs=50.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .=+||||+-|+.++++..|+..|..||.|+.++||.+..||+++|||||+|+.
T Consensus       100 Py~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~  152 (335)
T KOG0113|consen  100 PYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEH  152 (335)
T ss_pred             ccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEecc
Confidence            33899999999999999999999999999999999999999999999999974

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.54  E-value=4.8e-14  Score=82.75  Aligned_cols=54  Identities=35%  Similarity=0.470  Sum_probs=50.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+|||+|||+.+++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus       191 ~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~  244 (346)
T TIGR01659       191 IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNK  244 (346)
T ss_pred             cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECC
Confidence            345789999999999999999999999999999999998899999999999975

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.53  E-value=4.9e-14  Score=87.16  Aligned_cols=53  Identities=28%  Similarity=0.513  Sum_probs=50.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+.+++++|+++|..||.|.+++++.++.+++++|||||+|.+
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s  158 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEV  158 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCc
Confidence            45799999999999999999999999999999999999999999999999986

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.53  E-value=7.6e-14  Score=85.98  Aligned_cols=54  Identities=24%  Similarity=0.395  Sum_probs=50.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||+++++++|+++|..+|.|.+++++.+ .+++++|||||+|.+
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~  108 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCG  108 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCC
Confidence            345689999999999999999999999999999999999 799999999999986

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0126|consensus

Probab=99.51  E-value=6.5e-15  Score=79.61  Aligned_cols=56  Identities=32%  Similarity=0.475  Sum_probs=51.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +...+.-|||||||+..++.+|.-.|++||++..+.+++|..||+++||||+.|+.
T Consensus        31 ~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYED   86 (219)
T KOG0126|consen   31 EYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYED   86 (219)
T ss_pred             hcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecC
Confidence            34556889999999999999999999999999999999999999999999999874

>KOG0122|consensus

Probab=99.51  E-value=7.5e-14  Score=78.10  Aligned_cols=55  Identities=33%  Similarity=0.555  Sum_probs=51.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+...+|-|.||+.++++++|+++|.+||.|.++++.+++.||.++|||||.|.+
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~s  240 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFES  240 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEec
Confidence            3455789999999999999999999999999999999999999999999999986

>PF00076 RRM_1: RNA recognition motif

Probab=99.50  E-value=1.3e-13  Score=63.87  Aligned_cols=48  Identities=33%  Similarity=0.553  Sum_probs=44.9

Q ss_pred             EEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        16 l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |||+|||.++++++|+++|..+|.+..+.+..+ .++..+|+|||+|.+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~   48 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFES   48 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESS
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcC
Confidence            799999999999999999999999999988887 688999999999986

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0121|consensus

Probab=99.49  E-value=8.4e-14  Score=71.80  Aligned_cols=55  Identities=29%  Similarity=0.630  Sum_probs=50.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++++||||||++.++++.+.++|+.+|.|.++.+-.++.+..+.|||||+|.+
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~   87 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYS   87 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEec
Confidence            3457899999999999999999999999999999999999899999999999975

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.46  E-value=4.5e-13  Score=80.28  Aligned_cols=53  Identities=28%  Similarity=0.432  Sum_probs=50.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||..+++.+|.++|..+|.|..+.++.++.+++++|||||+|.+
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~  140 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYD  140 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECC
Confidence            35799999999999999999999999999999999999999999999999976

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.46  E-value=3.8e-13  Score=83.33  Aligned_cols=52  Identities=21%  Similarity=0.376  Sum_probs=49.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+|||+|||.++++++|+++|+.||.|..++++.++.+++++|||||+|.+
T Consensus       204 ~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~  255 (612)
T TIGR01645       204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNN  255 (612)
T ss_pred             cceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECC
Confidence            4789999999999999999999999999999999999899999999999986

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.45  E-value=8.8e-13  Score=79.84  Aligned_cols=54  Identities=20%  Similarity=0.340  Sum_probs=50.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +...+|||+|||..+++++|+++|..||.|..+.++.+..+|.++|||||+|.+
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~  346 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKD  346 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECC
Confidence            345799999999999999999999999999999999998899999999999975

Members of this subfamily are found in plants, metazoa and fungi.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.44  E-value=8.4e-13  Score=61.55  Aligned_cols=48  Identities=38%  Similarity=0.598  Sum_probs=43.0

Q ss_pred             EEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        16 l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |||+|||+++++++|..+|..+|.|..+.+...+. +..+|+|||+|.+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~   48 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSS   48 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESS
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCC
Confidence            79999999999999999999999999999998876 8999999999986

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.43  E-value=7.5e-13  Score=81.18  Aligned_cols=51  Identities=31%  Similarity=0.426  Sum_probs=48.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+|||+|||.++++++|+++|..+|.|.++++..+..+++++|||||+|.+
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~   51 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQN   51 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECC
Confidence            379999999999999999999999999999999999899999999999976

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.42  E-value=1.4e-12  Score=73.94  Aligned_cols=49  Identities=18%  Similarity=0.365  Sum_probs=44.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||+.+++++|+++|+.||.|.++.++.++.   .+|||||+|.+
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d   52 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKD   52 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCc
Confidence            47999999999999999999999999999999988753   57999999975

>PLN03213 repressor of silencing 3; Provisional

Probab=99.39  E-value=1.9e-12  Score=78.66  Aligned_cols=50  Identities=30%  Similarity=0.436  Sum_probs=45.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+||||||++.+++++|+..|..||.|.++.++  +.+|  ||||||+|.+
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMss   57 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSP   57 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecC
Confidence            345799999999999999999999999999999998  4677  9999999975

>KOG0117|consensus

Probab=99.37  E-value=3.1e-12  Score=76.50  Aligned_cols=55  Identities=24%  Similarity=0.416  Sum_probs=51.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++.||||.||.++.+++|..+|...|.|-+++|++|+.+|.+||||||.|-+
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~  134 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCT  134 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeec
Confidence            3566899999999999999999999999999999999999999999999999965

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.36  E-value=4.4e-12  Score=71.18  Aligned_cols=51  Identities=27%  Similarity=0.400  Sum_probs=45.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+.+|+|+||++.+++++|+++|+.||.|.++.++.+.   ..+++|||+|.+
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d   53 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKD   53 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECC
Confidence            345899999999999999999999999999999998874   445899999975

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.36  E-value=4.1e-12  Score=76.21  Aligned_cols=52  Identities=35%  Similarity=0.652  Sum_probs=49.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||..+++++|+++|..||.|..+.++.+..+|+++|||||+|.+
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~  237 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHD  237 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECC
Confidence            5899999999999999999999999999999999998899999999999975

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.35  E-value=8.9e-12  Score=68.90  Aligned_cols=52  Identities=44%  Similarity=0.649  Sum_probs=49.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+|||+|||+.+++++|...|..+|.+..+.+..++.+++.+|+|||+|.+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~  166 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFES  166 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecC
Confidence            4899999999999999999999999999999999998899999999999975

>KOG0131|consensus

Probab=99.35  E-value=2e-12  Score=69.94  Aligned_cols=56  Identities=27%  Similarity=0.463  Sum_probs=52.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.++..+||++||+..+++..|.++|.+.|.+..++++.++.+.+++||||++|.+
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~   60 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRT   60 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEec
Confidence            55677999999999999999999999999999999999999999999999999976

>KOG0124|consensus

Probab=99.33  E-value=1e-12  Score=77.45  Aligned_cols=53  Identities=28%  Similarity=0.518  Sum_probs=50.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEeeC
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF   65 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~   65 (65)
                      .+++|||++.+...++.++.-|.+||.|+.+.+.+|+.|+++|||+||+|+-+
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvP  165 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVP  165 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCc
Confidence            47999999999999999999999999999999999999999999999999853

>KOG0145|consensus

Probab=99.33  E-value=8.7e-13  Score=74.93  Aligned_cols=63  Identities=30%  Similarity=0.396  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         2 ~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ||.+|..+.....+|||++||..++..+|+++|++||.|...++..|..+|.++|.|||.|++
T Consensus       116 SyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDK  178 (360)
T KOG0145|consen  116 SYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDK  178 (360)
T ss_pred             EeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecc
Confidence            567777788888999999999999999999999999999888888888999999999999986

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.32  E-value=1e-11  Score=76.28  Aligned_cols=53  Identities=36%  Similarity=0.490  Sum_probs=49.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+|||+||+..+++++|+++|+.||.|.++.++.+ .++.++|||||+|.+
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~  335 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSN  335 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCC
Confidence            34578999999999999999999999999999999998 689999999999986

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0144|consensus

Probab=99.32  E-value=5.3e-12  Score=75.34  Aligned_cols=54  Identities=31%  Similarity=0.523  Sum_probs=50.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+.-++|||-+|+.++|.+|+++|++||.|.++.+++|+-++..+|||||.|.+
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~t   85 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYT   85 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEecc
Confidence            334689999999999999999999999999999999999999999999999976

>KOG0111|consensus

Probab=99.30  E-value=1.7e-12  Score=72.28  Aligned_cols=55  Identities=31%  Similarity=0.414  Sum_probs=51.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++||||+|...+++.-|..-|.+||.|.++.++.|-++++++|||||+|+-
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~   61 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEE   61 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeec
Confidence            3445899999999999999999999999999999999999999999999999973

>KOG0130|consensus

Probab=99.29  E-value=6.3e-12  Score=65.54  Aligned_cols=60  Identities=25%  Similarity=0.327  Sum_probs=55.2

Q ss_pred             CCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEeeC
Q psy7053           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF   65 (65)
Q Consensus         6 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~   65 (65)
                      .|++...+..|||.++...+++++++..|..||.|+.+++-.++.||..+||+.|+|+|.
T Consensus        65 gPqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~  124 (170)
T KOG0130|consen   65 GPQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETL  124 (170)
T ss_pred             CCccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhH
Confidence            356667778999999999999999999999999999999999999999999999999873

>KOG0125|consensus

Probab=99.29  E-value=1.1e-11  Score=71.95  Aligned_cols=54  Identities=35%  Similarity=0.528  Sum_probs=46.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+..++|+|+|||+...+.||+.+|.+||.|.++-++..  ..-+||||||.|+.
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen  145 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMEN  145 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecC
Confidence            3455689999999999999999999999999999988764  34478999999975

>KOG4205|consensus

Probab=99.27  E-value=1.4e-11  Score=71.55  Aligned_cols=53  Identities=38%  Similarity=0.545  Sum_probs=50.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+++||++|+|.++++.|++.|..+|++.+|.+++++.++..+||+||+|++
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~   57 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFAT   57 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCC
Confidence            66899999999999999999999999999999999999999999999999985

>smart00362 RRM_2 RNA recognition motif

Probab=99.26  E-value=4.7e-11  Score=54.67  Aligned_cols=48  Identities=38%  Similarity=0.662  Sum_probs=43.6

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +|+|+|+|..+++++|+++|..+|.+..+.+..++  +.++|+|||+|.+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~   48 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFES   48 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCC
Confidence            58999999999999999999999999998887765  7788999999976

>KOG0127|consensus

Probab=99.26  E-value=2.8e-11  Score=74.04  Aligned_cols=53  Identities=34%  Similarity=0.474  Sum_probs=50.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+|||.|||++++++.|...|+.||.|..+.++.++.|+.++|.|||.|.|
T Consensus       291 ~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt  343 (678)
T KOG0127|consen  291 EGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKT  343 (678)
T ss_pred             ccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEecc
Confidence            34899999999999999999999999999999999999999999999999976

>KOG0148|consensus

Probab=99.25  E-value=1.8e-11  Score=69.72  Aligned_cols=52  Identities=31%  Similarity=0.446  Sum_probs=48.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      -..+|++.|...++.++|++.|.+||+|.++++++|..|+|+||||||.|..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~  113 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPN  113 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccc
Confidence            3579999999999999999999999999999999999999999999999863

>KOG0108|consensus

Probab=99.22  E-value=2.6e-11  Score=72.98  Aligned_cols=51  Identities=27%  Similarity=0.432  Sum_probs=49.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.+||||+|++.+++.|..+|...|.|..++++.|+.+|+.+||||++|.+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~   69 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTD   69 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCc
Confidence            889999999999999999999999999999999999999999999999975

>smart00360 RRM RNA recognition motif

Probab=99.21  E-value=9.2e-11  Score=53.49  Aligned_cols=47  Identities=36%  Similarity=0.620  Sum_probs=43.1

Q ss_pred             EecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        18 v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |+|||..+++++|+++|..+|.+..+.+..++.++.++|+|||+|.+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~   47 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFES   47 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCC
Confidence            57899999999999999999999999888877789999999999976

>KOG0107|consensus

Probab=99.21  E-value=5e-11  Score=64.27  Aligned_cols=50  Identities=32%  Similarity=0.553  Sum_probs=42.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEeeC
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF   65 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~   65 (65)
                      ...++||||||+..+++.+|+..|..||.+..+.+..     .+.|||||+|+.+
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvAr-----nPPGfAFVEFed~   57 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVAR-----NPPGFAFVEFEDP   57 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEee-----cCCCceEEeccCc
Confidence            3468999999999999999999999999998876544     3579999999864

>KOG0124|consensus

Probab=99.18  E-value=9.5e-11  Score=69.34  Aligned_cols=51  Identities=22%  Similarity=0.372  Sum_probs=48.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++||.++..+.+++|++..|+.||.|.+|.+.+++..+.++||||++|..
T Consensus       211 nRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n  261 (544)
T KOG0124|consen  211 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNN  261 (544)
T ss_pred             heEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEecc
Confidence            589999999999999999999999999999999999899999999999975

>KOG0144|consensus

Probab=99.16  E-value=1.9e-11  Score=73.06  Aligned_cols=51  Identities=37%  Similarity=0.552  Sum_probs=48.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++||||.|+..++|.+++++|.+||.|.+|+++++. .+.+|||+||.|++
T Consensus       124 e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fst  174 (510)
T KOG0144|consen  124 ERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFST  174 (510)
T ss_pred             chhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEeh
Confidence            5789999999999999999999999999999999995 89999999999986

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.14  E-value=2.1e-10  Score=69.74  Aligned_cols=46  Identities=20%  Similarity=0.172  Sum_probs=41.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++.|||+|||+.+++++|+++|+.||.|..+.++.      .+|+|||+|++
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~------~k~~afVef~~   47 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP------GKRQALVEFED   47 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC------CCCEEEEEeCc
Confidence            47899999999999999999999999999998764      35899999986

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.11  E-value=8.5e-10  Score=50.65  Aligned_cols=49  Identities=43%  Similarity=0.628  Sum_probs=43.6

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +|++++||..++++++++.|..+|.+..+.+..++.+ .++|++||+|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s   49 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFED   49 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECC
Confidence            4899999999999999999999999999988877544 778999999976

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG0148|consensus

Probab=99.08  E-value=5.7e-10  Score=63.71  Aligned_cols=50  Identities=28%  Similarity=0.458  Sum_probs=44.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++||+||++...+++.+++.|.+||.|.++++-.+      +||+||.|+|
T Consensus       160 ssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~t  209 (321)
T KOG0148|consen  160 SSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFET  209 (321)
T ss_pred             CCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecc
Confidence            4455689999999999999999999999999999987665      5999999986

>KOG0114|consensus

Probab=99.08  E-value=1.2e-09  Score=54.79  Aligned_cols=52  Identities=31%  Similarity=0.440  Sum_probs=44.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++..+-|||.|||+.++.++..++|..||.|..+++-.   +...+|-|||.|+.
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~---~k~TrGTAFVVYed   66 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGN---TKETRGTAFVVYED   66 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecC---ccCcCceEEEEehH
Confidence            34557899999999999999999999999999988765   44568999999874

>KOG0105|consensus

Probab=99.07  E-value=5.3e-10  Score=61.11  Aligned_cols=52  Identities=19%  Similarity=0.266  Sum_probs=43.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEeeC
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF   65 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~   65 (65)
                      ...++|||+|||.++.+.+++.+|-+||.|..+.|-..   .-...||||+|+.+
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~   55 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDP   55 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCc
Confidence            44589999999999999999999999999999877432   23468999999863

>KOG0127|consensus

Probab=99.03  E-value=7.2e-10  Score=68.08  Aligned_cols=51  Identities=25%  Similarity=0.462  Sum_probs=48.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEe
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL   63 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~   63 (65)
                      +.||||++||++++.++|..+|+..|.|..+.++.+..++.++|||||.|.
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFa   55 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFA   55 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeee
Confidence            489999999999999999999999999999999999989999999999996

>KOG0146|consensus

Probab=99.02  E-value=3.8e-10  Score=64.57  Aligned_cols=55  Identities=29%  Similarity=0.419  Sum_probs=49.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +....++||||.|...-.|++++++|..||.|++|.+.+.+ .|.+||++||.|.+
T Consensus        15 rg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s   69 (371)
T KOG0146|consen   15 RGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSS   69 (371)
T ss_pred             CCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEecc
Confidence            33456899999999999999999999999999999888775 78999999999975

>KOG0147|consensus

Probab=99.02  E-value=2.4e-10  Score=69.71  Aligned_cols=50  Identities=34%  Similarity=0.616  Sum_probs=47.5

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +||+|||++++++++++.+|.+||.|..+.++.+..||.++||||++|..
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~  329 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVN  329 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEec
Confidence            39999999999999999999999999999999998899999999999964

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.01  E-value=3.2e-09  Score=64.65  Aligned_cols=48  Identities=19%  Similarity=0.212  Sum_probs=42.8

Q ss_pred             CCcEEEEecCCC-CCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+|||+||++ .+++++|+.+|+.||.|.++.++.+     .+|+|||+|.+
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~-----~~g~afV~f~~  322 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN-----KKETALIEMAD  322 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC-----CCCEEEEEECC
Confidence            457999999998 6999999999999999999988775     26999999975

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.96  E-value=3.9e-09  Score=52.43  Aligned_cols=51  Identities=22%  Similarity=0.399  Sum_probs=45.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhc--cCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFER--CGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~--~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .||++.|+|...+..+|.+++..  .|....+.++.|..++.+.|||||.|.+
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~   54 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTS   54 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCC
Confidence            58999999999999999888875  4778889999999999999999999975

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4208|consensus

Probab=98.96  E-value=3.9e-09  Score=58.16  Aligned_cols=54  Identities=24%  Similarity=0.333  Sum_probs=47.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcc-CCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERC-GEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~-g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....-+++..+|....+..+...|.++ |.+.+.++.+.+.||.++|||||+|++
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs  101 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFES  101 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEecc
Confidence            334568899999999999999999887 788888888999999999999999986

>KOG0146|consensus

Probab=98.94  E-value=2.7e-09  Score=61.16  Aligned_cols=57  Identities=21%  Similarity=0.181  Sum_probs=53.3

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+..++++|||=.||.+..+.+|.++|-+||.|...++-.|+.|..+|.||||.|+.
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDN  336 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDN  336 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCC
Confidence            366778999999999999999999999999999999999999999999999999975

>KOG0145|consensus

Probab=98.93  E-value=7.2e-09  Score=59.27  Aligned_cols=57  Identities=26%  Similarity=0.316  Sum_probs=51.3

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....+..+||=||..++++..|-++|.+||.+..+.+++|..+.+.||||||....
T Consensus       273 ~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtN  329 (360)
T KOG0145|consen  273 GGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTN  329 (360)
T ss_pred             CCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecc
Confidence            344556899999999999999999999999999999999999999999999997643

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=98.90  E-value=8e-09  Score=62.83  Aligned_cols=48  Identities=15%  Similarity=0.225  Sum_probs=37.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccC------------CEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCG------------EVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g------------~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+.+++++|.++|..++            .|..+.      .++.+|||||+|.+
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~------~~~~kg~afVeF~~  232 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVN------INKEKNFAFLEFRT  232 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEE------ECCCCCEEEEEeCC
Confidence            3458999999999999999999998741            222222      34568999999986

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=98.88  E-value=9.2e-09  Score=64.00  Aligned_cols=44  Identities=30%  Similarity=0.366  Sum_probs=39.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcc--CCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERC--GEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~--g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+||++++++++|+++|+.|  |.|.++.++        ++||||+|.+
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s  278 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFED  278 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCC
Confidence            4789999999999999999999999  999988653        4699999986

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0131|consensus

Probab=98.86  E-value=2.8e-09  Score=57.95  Aligned_cols=55  Identities=25%  Similarity=0.261  Sum_probs=48.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEE-EEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+.+.++|++||.+.+++..|...|+.||.+.+. .+++++.||.++|+||+.|++
T Consensus        93 l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~s  148 (203)
T KOG0131|consen   93 LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYAS  148 (203)
T ss_pred             ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechh
Confidence            3455899999999999999999999999987653 567888899999999999876

>KOG4205|consensus

Probab=98.81  E-value=2.6e-08  Score=58.14  Aligned_cols=52  Identities=35%  Similarity=0.512  Sum_probs=49.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|+++||.++++.++++.|.++|.|..+.++.|..+.+++||+||.|.+
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~  148 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDS  148 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEecc
Confidence            4689999999999999999999999999999999999999999999999875

>KOG0415|consensus

Probab=98.79  E-value=8.3e-09  Score=61.02  Aligned_cols=51  Identities=33%  Similarity=0.385  Sum_probs=48.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .-|||..|++.+++++|.-+|+.||.|..|.++++..||.+-.||||+|+.
T Consensus       240 NVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen  290 (479)
T KOG0415|consen  240 NVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFEN  290 (479)
T ss_pred             ceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecc
Confidence            579999999999999999999999999999999999999999999999974

>KOG0110|consensus

Probab=98.74  E-value=1.2e-08  Score=63.95  Aligned_cols=53  Identities=25%  Similarity=0.501  Sum_probs=48.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEeeC
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF   65 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~   65 (65)
                      ..+|+|.|+|+.++...++.+|..||++..++++.....+.++|||||+|.|+
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~  665 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTP  665 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCc
Confidence            57899999999999999999999999999999987766788899999999773

>KOG4212|consensus

Probab=98.74  E-value=5.8e-08  Score=58.86  Aligned_cols=50  Identities=26%  Similarity=0.347  Sum_probs=46.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhc-cCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFER-CGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~-~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.+||.|+|+++.+.+|++++.. .|+|..+.+..|. +||++|+|.|+|.+
T Consensus        45 R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~   95 (608)
T KOG4212|consen   45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKD   95 (608)
T ss_pred             ceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeC
Confidence            56999999999999999999985 7999999999994 99999999999976

>KOG0123|consensus

Probab=98.72  E-value=3.8e-08  Score=58.61  Aligned_cols=47  Identities=21%  Similarity=0.356  Sum_probs=43.6

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+||.||+.+++..+|.++|+.||.|..|.+..+. .| ++|| ||+|++
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~  124 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFES  124 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCC
Confidence            39999999999999999999999999999999985 55 8999 999986

>KOG0117|consensus

Probab=98.70  E-value=7.1e-08  Score=58.30  Aligned_cols=53  Identities=21%  Similarity=0.310  Sum_probs=41.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCC-EEEEEEeec-CCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIPRD-RFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~-i~~~~~~~~-~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||||+|...+++++.+.+...++ +.++-+..+ -+..+++|||||+|++
T Consensus       163 an~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~  217 (506)
T KOG0117|consen  163 ANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYES  217 (506)
T ss_pred             ecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeec
Confidence            4589999999999999999999987654 444434333 2568899999999975

>KOG0116|consensus

Probab=98.68  E-value=7.1e-08  Score=58.20  Aligned_cols=52  Identities=25%  Similarity=0.310  Sum_probs=43.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+||+.|||.+++...|++.|..||.|+...+......++..+||||+|.+
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~  339 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFEN  339 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEee
Confidence            3569999999999999999999999999988765543345555999999975

>smart00361 RRM_1 RNA recognition motif

Probab=98.65  E-value=1.1e-07  Score=44.45  Aligned_cols=38  Identities=32%  Similarity=0.496  Sum_probs=31.3

Q ss_pred             HHHHHHHhh----ccCCEEEEE-EeecCCC--CCcccEEEEEEee
Q psy7053          27 PDDLRRVFE----RCGEVGDIY-IPRDRFT--RESRGFAFVRLLL   64 (65)
Q Consensus        27 ~~~l~~~f~----~~g~i~~~~-~~~~~~~--~~~~g~~fv~f~~   64 (65)
                      +++|++.|.    .||.+.++. ++.++.+  +.++|++||.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~   46 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFER   46 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECC
Confidence            467777787    999999985 6777666  8999999999976

>KOG0109|consensus

Probab=98.65  E-value=4.5e-08  Score=56.60  Aligned_cols=42  Identities=33%  Similarity=0.552  Sum_probs=36.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEe
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL   63 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~   63 (65)
                      .+|||||||..+++..|+.+|++||++.+|.++.        .||||.-+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK--------NYgFVHiE   44 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVK--------NYGFVHIE   44 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeec--------ccceEEee
Confidence            5799999999999999999999999999998865        36777654

>KOG4209|consensus

Probab=98.57  E-value=7.1e-08  Score=54.38  Aligned_cols=56  Identities=27%  Similarity=0.553  Sum_probs=50.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .......+|++|+.+.++...++.-|+.||.+..+.++.+...+.++||+||+|..
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~  152 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSS  152 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEeccc
Confidence            34455899999999999998899999999999989999999899999999999975

>KOG0123|consensus

Probab=98.51  E-value=3.4e-07  Score=54.62  Aligned_cols=54  Identities=28%  Similarity=0.394  Sum_probs=48.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....+|||.|++..++++.|+..|+.+|.|..++++.+ ..++++||+||+|++
T Consensus       267 ~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~-~~g~skG~gfV~fs~  320 (369)
T KOG0123|consen  267 SLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVD-ENGKSKGFGFVEFSS  320 (369)
T ss_pred             cccccccccccCccccchhHHHHHHhcccceeeEEEEec-cCCCccceEEEEcCC
Confidence            445589999999999999999999999999999888877 489999999999986

>KOG4206|consensus

Probab=98.47  E-value=1e-06  Score=49.19  Aligned_cols=48  Identities=33%  Similarity=0.490  Sum_probs=41.2

Q ss_pred             cEEEEecCCCCCCHHHHHH----HhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~----~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+|||.||+..+..++|++    +|+.||.|.++....   +.+.+|-|||.|..
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~   61 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKE   61 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecC
Confidence            4999999999999888776    999999998875433   78899999999964

>KOG0226|consensus

Probab=98.45  E-value=2.3e-07  Score=52.86  Aligned_cols=55  Identities=24%  Similarity=0.310  Sum_probs=48.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+...+||+|.|..+.+++.|.+.|..|-......++++..||+++||+||.|.+
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~  241 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRD  241 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecC
Confidence            3456899999999999999999999998877777889999999999999999975

>KOG0153|consensus

Probab=98.36  E-value=1.3e-06  Score=51.60  Aligned_cols=51  Identities=27%  Similarity=0.424  Sum_probs=43.1

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++.....+|||++|...+.+.+|+.-|-+||+|..+.++..      +++|||.|.|
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftT  273 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTT  273 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehh
Confidence            34455589999999999999999999999999998876553      4699999976

>KOG0132|consensus

Probab=98.30  E-value=1.5e-06  Score=55.65  Aligned_cols=45  Identities=31%  Similarity=0.541  Sum_probs=39.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEe
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL   63 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~   63 (65)
                      ++|||||.|+..+++.+|..+|+.||+|.++.+.-      ++|+|||...
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~  465 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMV  465 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEe
Confidence            48999999999999999999999999999986644      5689998753

>KOG0106|consensus

Probab=98.26  E-value=1.1e-06  Score=49.21  Aligned_cols=43  Identities=28%  Similarity=0.532  Sum_probs=37.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+||+++|+.+.+.++..+|..+|.+..+.+..        ||+||+|+.
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed   44 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFED   44 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCc
Confidence            4789999999999999999999999998876533        788999875

>KOG4454|consensus

Probab=98.21  E-value=7.9e-07  Score=49.90  Aligned_cols=54  Identities=26%  Similarity=0.327  Sum_probs=45.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+..++|||+|+-..++++.|.++|.+.|.|.++.+..++ .++.+ |+||+|..
T Consensus         5 aae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~   58 (267)
T KOG4454|consen    5 AAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPN   58 (267)
T ss_pred             CcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeeccc
Confidence            34556899999999999999999999999999998887765 55666 99999863

>KOG4212|consensus

Probab=98.20  E-value=3e-06  Score=51.69  Aligned_cols=52  Identities=25%  Similarity=0.246  Sum_probs=43.8

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+.++|+|.|||++.++..|++.|..+|.+....++   +.|+++|  .|.|.+
T Consensus       531 gaarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s  582 (608)
T KOG4212|consen  531 GAARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFS  582 (608)
T ss_pred             cccccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecC
Confidence            345667899999999999999999999999999887763   4788887  677765

>KOG0533|consensus

Probab=98.14  E-value=1.1e-05  Score=45.91  Aligned_cols=51  Identities=29%  Similarity=0.406  Sum_probs=44.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+|+|.|||..+.+++|+++|..+|.+..+.+..++ +|.+.|.|-|.|..
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r  133 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNR  133 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecc
Confidence            3789999999999999999999999988887777775 89999999888864

>KOG4661|consensus

Probab=98.11  E-value=9.1e-06  Score=51.15  Aligned_cols=52  Identities=23%  Similarity=0.338  Sum_probs=45.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +++|||.+|...+...+|+.+|++||.|.-..++....+.-.+.|+||...|
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSt  456 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMST  456 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecc
Confidence            4799999999999999999999999999888888776666778999998875

>KOG0120|consensus

Probab=98.08  E-value=8.2e-06  Score=50.36  Aligned_cols=56  Identities=21%  Similarity=0.318  Sum_probs=51.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .......+++++||...++..+.++...+|.+....++.+..+|.++||+|.+|-.
T Consensus       285 ~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~d  340 (500)
T KOG0120|consen  285 VPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCD  340 (500)
T ss_pred             cccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeC
Confidence            44556789999999999999999999999999999999999999999999999865

>KOG4849|consensus

Probab=98.03  E-value=2.5e-06  Score=50.78  Aligned_cols=50  Identities=28%  Similarity=0.423  Sum_probs=41.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccC--CEEEEEEeecCCCCCcccEEEEEEe
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRLL   63 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~~fv~f~   63 (65)
                      ..+|||||.|++++++|.+-+...|  .+.++.+-..+.+|++||||.+...
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~  132 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLN  132 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEec
Confidence            4799999999999999988877655  5666667778889999999998654

>KOG0110|consensus

Probab=98.02  E-value=1.1e-05  Score=51.19  Aligned_cols=52  Identities=35%  Similarity=0.451  Sum_probs=41.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCC---CCcccEEEEEEeeC
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFT---RESRGFAFVRLLLF   65 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~---~~~~g~~fv~f~~~   65 (65)
                      .+||+.||+++++.+++...|...|.|..+.+...+..   -.+.|||||+|.++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~  570 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKP  570 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCH
Confidence            34999999999999999999999999988876654322   12349999999863

>KOG4211|consensus

Probab=97.99  E-value=4.4e-05  Score=46.94  Aligned_cols=53  Identities=19%  Similarity=0.397  Sum_probs=42.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.+...-|-+.+|||++++++|..+|+.++ |..+.+  .+.+|++.|=|||+|.+
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~--~r~~Gr~sGeA~Ve~~s   58 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEI--PRRNGRPSGEAYVEFTS   58 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEE--eccCCCcCcceEEEeec
Confidence            344456677889999999999999999885 655444  44689999999999975

>KOG0109|consensus

Probab=97.93  E-value=1.8e-05  Score=46.12  Aligned_cols=44  Identities=32%  Similarity=0.465  Sum_probs=39.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEe
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL   63 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~   63 (65)
                      ...+++|+|+.+.++.++++..|.++|.+..|.++.        +|+||.|+
T Consensus        77 ~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--------dy~fvh~d  120 (346)
T KOG0109|consen   77 ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--------DYAFVHFD  120 (346)
T ss_pred             CccccccCCCCccccCHHHhhhhcccCCceeeeeec--------ceeEEEEe
Confidence            447899999999999999999999999999998865        58999986

>PF13893 RRM_5: RNA recognition motif

Probab=97.92  E-value=3.8e-05  Score=34.13  Aligned_cols=30  Identities=43%  Similarity=0.744  Sum_probs=23.4

Q ss_pred             HHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          30 LRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        30 l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |.++|++||.|.++.+....     ++++||+|.+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~   30 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFAS   30 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESS
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECC
Confidence            57889999999998775532     6899999976

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG4660|consensus

Probab=97.88  E-value=3.7e-05  Score=47.75  Aligned_cols=47  Identities=34%  Similarity=0.445  Sum_probs=40.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|+|-|||..+++++|+++|+.+|+|..++.     +...+|..||+|-+
T Consensus        75 ~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyD  121 (549)
T KOG4660|consen   75 QGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYD  121 (549)
T ss_pred             cceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEee
Confidence            379999999999999999999999999987543     55667999999965

>KOG0129|consensus

Probab=97.79  E-value=0.00011  Score=45.43  Aligned_cols=53  Identities=17%  Similarity=0.253  Sum_probs=40.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecC---CCCCccc---EEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR---FTRESRG---FAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~---~~~~~~g---~~fv~f~~   64 (65)
                      .-+++||+|+||++++|+.+...|..||.+ .+.++...   .---++|   |+|+.|+.
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~  315 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFED  315 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecc
Confidence            445899999999999999999999999987 45565211   1122356   99999874

>KOG4210|consensus

Probab=97.73  E-value=1.8e-05  Score=46.00  Aligned_cols=53  Identities=30%  Similarity=0.533  Sum_probs=47.1

Q ss_pred             CCcEEE-EecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLK-VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~-v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+++ ++++++.+++++|+..|..+|.|..++++.++.++..+|++++.|..
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~  236 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSA  236 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhh
Confidence            345666 99999999999999889999999999999999999999999998753

>KOG1548|consensus

Probab=97.73  E-value=0.0003  Score=41.90  Aligned_cols=53  Identities=23%  Similarity=0.342  Sum_probs=42.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEE--------EEEEeecCCCCCcccEEEEEEe
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVG--------DIYIPRDRFTRESRGFAFVRLL   63 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~~fv~f~   63 (65)
                      ......|||+|||.+++.+.+.++++.||-|.        +|.+-++. .|+.+|=|.+.|.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~  191 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYI  191 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEee
Confidence            34446799999999999999999999999664        35666664 5888998887774

>KOG4211|consensus

Probab=97.72  E-value=0.00025  Score=43.82  Aligned_cols=55  Identities=24%  Similarity=0.344  Sum_probs=42.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEE-EEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD-IYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .......|-+.+||+.+++++|.++|+..--+.. +.++.++ .+++.|-|||.|++
T Consensus        99 s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~s  154 (510)
T KOG4211|consen   99 SSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFES  154 (510)
T ss_pred             CCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecC
Confidence            3345567889999999999999999997643333 4456664 67788999999986

>KOG0151|consensus

Probab=97.63  E-value=0.00012  Score=47.03  Aligned_cols=53  Identities=28%  Similarity=0.365  Sum_probs=42.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecC---CCCCcccEEEEEEe
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR---FTRESRGFAFVRLL   63 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~---~~~~~~g~~fv~f~   63 (65)
                      +...++|++||+..++++.|-..|..||.+..+.++..+   +....+-+|||.|-
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafm  227 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFM  227 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeeh
Confidence            344789999999999999999999999999888877654   22334467788774

>KOG0129|consensus

Probab=97.63  E-value=0.00037  Score=43.23  Aligned_cols=57  Identities=21%  Similarity=0.164  Sum_probs=49.4

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhh-ccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFE-RCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~-~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+..+|||||+||.-.+...|..++. -||.|..+.+=.|++=+-++|-|=|.|..
T Consensus       365 q~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsn  422 (520)
T KOG0129|consen  365 QPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSN  422 (520)
T ss_pred             cccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecc
Confidence            3556669999999999999999999999 59999888887887788889988888864

>KOG0147|consensus

Probab=97.57  E-value=1.8e-05  Score=49.08  Aligned_cols=52  Identities=33%  Similarity=0.477  Sum_probs=47.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+++|+--++...+.-+|.++|+..|.|.+++++.++.++..+|.+||+|..
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D  230 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCD  230 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEec
Confidence            3678888788888899999999999999999999999999999999999964

>KOG1457|consensus

Probab=97.57  E-value=0.0004  Score=39.50  Aligned_cols=55  Identities=15%  Similarity=0.193  Sum_probs=39.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEee-cCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPR-DRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~-~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||.+||.++-.-.|.-+|..|..-.-+.+-. ++...-.+-+||+.|.+
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s   86 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTS   86 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecc
Confidence            34469999999999999999999999875443333322 22222334799999975

>KOG1457|consensus

Probab=97.27  E-value=0.00026  Score=40.19  Aligned_cols=50  Identities=20%  Similarity=0.175  Sum_probs=36.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+|||.||..+++++.|+++|+.|.....+++..  ..|  ...+|++|+.
T Consensus       208 ~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~--~~g--~~vaf~~~~~  257 (284)
T KOG1457|consen  208 RACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA--RGG--MPVAFADFEE  257 (284)
T ss_pred             hhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec--CCC--cceEeecHHH
Confidence            3446899999999999999999999986554444422  122  3578888863

>KOG1995|consensus

Probab=96.94  E-value=0.0023  Score=38.23  Aligned_cols=57  Identities=21%  Similarity=0.148  Sum_probs=47.4

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEE--------EEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD--------IYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~--------~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .......++||-+||..++++++.+.|.+++.|..        +.+-.+++|++.||=|.|.|++
T Consensus        61 ~~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D  125 (351)
T KOG1995|consen   61 ADKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYED  125 (351)
T ss_pred             ccccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecC
Confidence            34455578999999999999999999999997753        4556778999999999998875

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=96.94  E-value=0.0049  Score=31.04  Aligned_cols=45  Identities=27%  Similarity=0.430  Sum_probs=27.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +-|.+.+++..++.++|+..|..+|.|..+.+...    .  --|+|.|.+
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G----~--~~g~VRf~~   46 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG----D--TEGYVRFKT   46 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC----C--CEEEEEECC
Confidence            45788889999999999999999999988876442    2  356888865

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1190|consensus

Probab=96.90  E-value=0.0016  Score=39.88  Aligned_cols=47  Identities=17%  Similarity=0.273  Sum_probs=37.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++-+.++|||++++|.++.++..+||.+..+.+...    ++  -+|+++.+
T Consensus        27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkG----kn--QAflem~d   73 (492)
T KOG1190|consen   27 PSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKG----KN--QAFLEMAD   73 (492)
T ss_pred             CcceeEeccCCccccHHHHHHhcccccceeeeeeecc----ch--hhhhhhcc
Confidence            4578999999999999999999999999988765432    22  56777654

>KOG4206|consensus

Probab=96.87  E-value=0.0062  Score=34.43  Aligned_cols=48  Identities=25%  Similarity=0.330  Sum_probs=40.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+++.|+|..++.+.+..+|.+|.....++++...     .+.+||+|.+
T Consensus       145 pn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~  192 (221)
T KOG4206|consen  145 PNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLS  192 (221)
T ss_pred             CceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecch
Confidence            34689999999999999999999999888888876542     4789999975

>KOG0128|consensus

Probab=96.78  E-value=0.00094  Score=43.66  Aligned_cols=50  Identities=18%  Similarity=0.327  Sum_probs=45.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|.|.|+..+.+.++.++...|.+...+++..+ .|+++|.+++.|.+
T Consensus       737 ~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~  786 (881)
T KOG0128|consen  737 ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNT  786 (881)
T ss_pred             hhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCC
Confidence            568999999999999999999999999998877765 89999999999875

>KOG3152|consensus

Probab=96.44  E-value=0.0076  Score=34.88  Aligned_cols=37  Identities=24%  Similarity=0.471  Sum_probs=32.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeec
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRD   48 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~   48 (65)
                      ..--||++++|+..+...|++++..||.|.++.+...
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE  109 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPE  109 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecch
Confidence            4467999999999999999999999999999987644

>KOG0105|consensus

Probab=96.35  E-value=0.033  Score=31.13  Aligned_cols=48  Identities=23%  Similarity=0.268  Sum_probs=38.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEe
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL   63 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~   63 (65)
                      ......+|.|.+||.+.++.+|+.-....|.+....+..+       |++.|+|.
T Consensus       111 srrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~  158 (241)
T KOG0105|consen  111 SRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYL  158 (241)
T ss_pred             ccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeee
Confidence            4444578999999999999999999999999987766554       46677764

>KOG0128|consensus

Probab=96.31  E-value=9.8e-05  Score=47.94  Aligned_cols=53  Identities=25%  Similarity=0.412  Sum_probs=45.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|++||+..+.+.++...|..+|.+..+++......++.+|+||++|..
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~  718 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLK  718 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeec
Confidence            34678999999999999999999999888777666566789999999999975

>KOG0115|consensus

Probab=95.57  E-value=0.014  Score=33.78  Aligned_cols=49  Identities=22%  Similarity=0.211  Sum_probs=40.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEe
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL   63 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~   63 (65)
                      ..|||.||+.-++.+.+.+-|+.||.+....+..| ..+++.+-++|+|.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~   80 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFA   80 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhh
Confidence            67999999999999999999999999987655555 36666676777765

>KOG2314|consensus

Probab=95.49  E-value=0.091  Score=33.77  Aligned_cols=52  Identities=23%  Similarity=0.369  Sum_probs=40.6

Q ss_pred             CCcEEEEecCCCCCCH------HHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTP------DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~------~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....|.|.|+|..-..      .-|..+|+.+|.+....++.+..+| .+||.|++|.+
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~  114 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYAS  114 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecC
Confidence            3467888999876543      3467889999999888888776555 99999999975

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=95.23  E-value=0.1  Score=23.05  Aligned_cols=44  Identities=25%  Similarity=0.464  Sum_probs=30.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.|-|.+.+.+..+..+. .|..+|+|.+..+.      ...-+.++.|.+
T Consensus         2 ~wI~V~Gf~~~~~~~vl~-~F~~fGeI~~~~~~------~~~~~~~l~y~~   45 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVLE-HFASFGEIVDIYVP------ESTNWMYLKYKS   45 (53)
T ss_pred             cEEEEEeECchHHHHHHH-HHHhcCCEEEEEcC------CCCcEEEEEECC
Confidence            466777777666555554 67789999988764      223467888865

>KOG4676|consensus

Probab=94.44  E-value=0.13  Score=31.79  Aligned_cols=51  Identities=16%  Similarity=0.273  Sum_probs=38.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecC-CC--CCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-FT--RESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~-~~--~~~~g~~fv~f~~   64 (65)
                      ..|-|.||..+++.++++.+|...|.|..+.|.-.. ..  ....-.|||.|..
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d   61 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLD   61 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccC
Confidence            478899999999999999999999999988765321 11  2223578888754

>KOG4307|consensus

Probab=94.29  E-value=0.072  Score=35.06  Aligned_cols=54  Identities=26%  Similarity=0.068  Sum_probs=42.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEE-EEEeecCCCCCcccEEEEEEe
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD-IYIPRDRFTRESRGFAFVRLL   63 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~~fv~f~   63 (65)
                      ..+....|||..||..+.+.++..+|...-.+.+ +.+... .+++.++-|||+|.
T Consensus       430 P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~  484 (944)
T KOG4307|consen  430 PGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFI  484 (944)
T ss_pred             CCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccC-Ccccccchhhheec
Confidence            3455678999999999999999999987555555 555444 47888899999986

>KOG4660|consensus

Probab=94.14  E-value=0.045  Score=34.67  Aligned_cols=50  Identities=24%  Similarity=0.354  Sum_probs=31.8

Q ss_pred             EEEEecCCCCCCHHHHHHHhh-ccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFE-RCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~-~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++.|.|++...+...|.+.-. ..|.-..+.++.|-.+.++.|||||.|..
T Consensus       390 t~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~s  440 (549)
T KOG4660|consen  390 TLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTS  440 (549)
T ss_pred             hhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecC
Confidence            344444444444444433322 24556667888998899999999998864

>KOG1365|consensus

Probab=94.14  E-value=0.33  Score=30.08  Aligned_cols=51  Identities=22%  Similarity=0.339  Sum_probs=37.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhc-c---CCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFER-C---GEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~-~---g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .-.|-+.+||+++++.++.++|.+ +   |....+.++.. ..|+..|=|||.|..
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~  215 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFAC  215 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecC
Confidence            356778899999999999999963 2   23334444443 478888999999864

>KOG4307|consensus

Probab=94.08  E-value=0.21  Score=33.02  Aligned_cols=52  Identities=15%  Similarity=0.122  Sum_probs=40.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+-|-+.|+|++++.+++-++|..|..+..-...+-.+.|+..|-+-|.|++
T Consensus       867 p~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes  918 (944)
T KOG4307|consen  867 PRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFES  918 (944)
T ss_pred             CeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecC
Confidence            3578889999999999999999998644332233444678888999999986

>KOG1365|consensus

Probab=94.01  E-value=0.077  Score=32.68  Aligned_cols=51  Identities=14%  Similarity=0.229  Sum_probs=40.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccC-CEEE--EEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCG-EVGD--IYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g-~i~~--~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...|-+.+||+.++.+++..+|..|- .|..  ++++.. ..|.+.|-|||++.+
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~n  333 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRN  333 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhh
Confidence            35788999999999999999998875 3443  556655 578889999998753

>KOG1855|consensus

Probab=93.67  E-value=0.28  Score=30.59  Aligned_cols=37  Identities=19%  Similarity=0.371  Sum_probs=33.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeec
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRD   48 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~   48 (65)
                      .+++|.+-|||.+-.-+.|.++|..+|.|+.+++...
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckP  266 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKP  266 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCC
Confidence            5689999999999999999999999999999987654

>KOG4410|consensus

Probab=92.50  E-value=0.82  Score=27.40  Aligned_cols=45  Identities=18%  Similarity=0.172  Sum_probs=32.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCE-EEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i-~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .-++++||+.++.-.+|+..+..-+.. .++.|  .   | +.|-||+.|..
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~~~pm~isw--k---g-~~~k~flh~~~  376 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRECTPMSISW--K---G-HFGKCFLHFGN  376 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcCCCceeEee--e---c-CCcceeEecCC
Confidence            469999999999999999988876533 23333  2   1 45668888753

>KOG0112|consensus

Probab=92.15  E-value=0.53  Score=31.89  Aligned_cols=49  Identities=18%  Similarity=0.237  Sum_probs=38.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEeeC
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF   65 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~   65 (65)
                      .....+|+++|..++....+.+.|..||.|..+.+-      +...|+++.|+++
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~------hgq~yayi~yes~  501 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR------HGQPYAYIQYESP  501 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeecc------cCCcceeeecccC
Confidence            345789999999999999999999999998776541      1235888887753

>KOG0106|consensus

Probab=91.15  E-value=0.18  Score=28.66  Aligned_cols=45  Identities=36%  Similarity=0.456  Sum_probs=35.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+.+.+.+++..+.+.+|...|.++|.+....+        ..+++||+|++
T Consensus        98 s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~  142 (216)
T KOG0106|consen   98 THFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSE  142 (216)
T ss_pred             ccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehh
Confidence            3467888899999999999999999998833322        35678999875

>KOG2416|consensus

Probab=90.84  E-value=0.15  Score=32.95  Aligned_cols=53  Identities=26%  Similarity=0.372  Sum_probs=39.3

Q ss_pred             CCCCCCCCcEEEEecCCCCCCHHHHHHHhhc-cCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFER-CGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         6 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~-~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +|.+...+..|+|.||-...+..+|+.++.. +|.|... |+ |    +.|..|||.|.|
T Consensus       437 SPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-D----kIKShCyV~yss  490 (718)
T KOG2416|consen  437 SPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-D----KIKSHCYVSYSS  490 (718)
T ss_pred             CCCCCCccceEeeecccccchHHHHHHHHhhccCchHHH-HH-H----HhhcceeEeccc
Confidence            4556667788999999999999999999985 5555444 32 2    245678888765

>KOG1456|consensus

Probab=90.26  E-value=2.7  Score=26.22  Aligned_cols=50  Identities=14%  Similarity=0.114  Sum_probs=37.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+--+.|.+|-..+++.+|-+-++.||.|..+.++-.      +..+.|+|+.
T Consensus        27 k~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~------~r~alvefed   76 (494)
T KOG1456|consen   27 KPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH------KRQALVEFED   76 (494)
T ss_pred             CCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc------cceeeeeecc
Confidence            3444567899999999999999999999999977654432      2346677763

>KOG0112|consensus

Probab=90.15  E-value=0.1  Score=35.03  Aligned_cols=52  Identities=27%  Similarity=0.491  Sum_probs=38.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEe
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL   63 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~   63 (65)
                      ...++||+||++...++.+++..|..+|.+.++.+-..+ -+.---|+|+.|.
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~  421 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLL  421 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhh
Confidence            345899999999999999999999999999888764432 1222245666654

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=89.56  E-value=1.5  Score=21.49  Aligned_cols=33  Identities=12%  Similarity=0.157  Sum_probs=22.3

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeec
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRD   48 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~   48 (65)
                      .+|--..|...-..+|.++|++||.| .+.++.+
T Consensus        10 HVFhltFPkeWK~~DI~qlFspfG~I-~VsWi~d   42 (87)
T PF08675_consen   10 HVFHLTFPKEWKTSDIYQLFSPFGQI-YVSWIND   42 (87)
T ss_dssp             CEEEEE--TT--HHHHHHHCCCCCCE-EEEEECT
T ss_pred             eEEEEeCchHhhhhhHHHHhccCCcE-EEEEEcC
Confidence            45555599999999999999999988 5555554

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=87.91  E-value=2.1  Score=21.08  Aligned_cols=41  Identities=32%  Similarity=0.515  Sum_probs=22.9

Q ss_pred             cEEEEecCCCCCCHHH----HHHHhhccC-CEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDD----LRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~----l~~~f~~~g-~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..|+|.|||-+.+...    |+++...+| .+..+       +   .+-|++.|.+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-------~---~~tAilrF~~   48 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-------S---GGTAILRFPN   48 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESS
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-------e---CCEEEEEeCC
Confidence            3589999999988655    556666776 44333       1   2567787764

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG1190|consensus

Probab=87.15  E-value=1.9  Score=27.03  Aligned_cols=31  Identities=19%  Similarity=0.363  Sum_probs=25.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEE
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGD   42 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~   42 (65)
                      .+.++...|+|.++++++++..|..-|...+
T Consensus       413 psatlHlsnip~svsee~lk~~f~~~g~~vk  443 (492)
T KOG1190|consen  413 PSATLHLSNIPPSVSEEDLKNLFQEPGGQVK  443 (492)
T ss_pred             chhheeeccCCcccchhHHHHhhhcCCceEE
Confidence            3468999999999999999999997665433

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=85.27  E-value=2.7  Score=25.92  Aligned_cols=32  Identities=13%  Similarity=0.256  Sum_probs=24.1

Q ss_pred             cEEEEecCCCCCCHHH------HHHHhhccCCEEEEEE
Q psy7053          14 VSLKVDNLTYRTTPDD------LRRVFERCGEVGDIYI   45 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~------l~~~f~~~g~i~~~~~   45 (65)
                      .-+||-+|+..+..+.      -.++|.+||.|.++.+
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvv  152 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVV  152 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEe
Confidence            4578888888776544      2588999999988754

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=84.78  E-value=2.3  Score=23.31  Aligned_cols=29  Identities=7%  Similarity=0.045  Sum_probs=19.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhc-cCCE
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFER-CGEV   40 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~-~g~i   40 (65)
                      ...+|-|+.||+..+++.+.+.+.. ++.-
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~   35 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDE   35 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccc
Confidence            3468999999999999999887765 5544

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG2193|consensus

Probab=84.55  E-value=0.83  Score=28.78  Aligned_cols=23  Identities=39%  Similarity=0.573  Sum_probs=20.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhc
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFER   36 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~   36 (65)
                      ..+|++||....+..++..+|..
T Consensus         2 nklyignL~p~~~psdl~svfg~   24 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGD   24 (584)
T ss_pred             CcccccccCCCCChHHHHHHhcc
Confidence            36899999999999999999875

>KOG4210|consensus

Probab=84.04  E-value=0.53  Score=27.77  Aligned_cols=54  Identities=13%  Similarity=-0.032  Sum_probs=40.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+++|++++.+.+.+.....++...|......+.........+|++++.|..
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~  139 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAG  139 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeecccc
Confidence            356889999999999988777777777765555554444577788999998864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	65
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		6e-25
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		3e-20
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		2e-17
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-05
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		4e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		4e-05
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		7e-05
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		9e-05
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		1e-04
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		2e-04
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		2e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		2e-04
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		2e-04
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		3e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		3e-04
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		3e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		3e-04
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		4e-04
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-04

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score =  108 bits (271), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 50/62 (80%), Positives = 56/62 (90%)
Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 35 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94
Query: 61 RL 62
          R 
Sbjct: 95 RF 96

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 93.2 bits (230), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 42/53 (79%), Positives = 48/53 (90%)
Query: 10  IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
           +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFVR 
Sbjct: 67  VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF 119

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 84.0 bits (206), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 39/61 (63%), Positives = 48/61 (78%)
Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          S G   P ++GM++LKVDNLTYRT+PD LRRVFE+ G VGD+YIPR+  T+  RGFAFVR
Sbjct: 2  SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61
Query: 62 L 62
Sbjct: 62 F 62

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 23/60 (38%), Positives = 32/60 (53%)
Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MS    P   E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV
Sbjct: 1  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL 64
          L V NL+Y ++ +DL ++F   G + +++ P D  T++ +GFAFV  + 
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMF 59

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 32/60 (53%)
Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MS    P   E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV
Sbjct: 1  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/46 (41%), Positives = 30/46 (65%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL 63
          V NL +  T +DL R+F + G+V  + I +D+ TR+S+G AF+  L
Sbjct: 21 VSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFL 66

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/55 (34%), Positives = 33/55 (60%)
Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          P  R +   +++V NL+  T   DL+ +F   G +  IY+ +D+ T +S+GFAF+
Sbjct: 8  PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 62

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 28/47 (59%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
          L V  L + TT + LR  F + GEV D  I +D+ T +SRGF FV+ 
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 31/59 (52%)
Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          S    P   E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV
Sbjct: 3  SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 61

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 28/46 (60%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL 63
          +  L+++TT + LR  F + GEV +  + RD  T+ SRGF FV  +
Sbjct: 30 IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 75

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 28/45 (62%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 31/59 (52%)
Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          S    P   E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV
Sbjct: 1  SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 59

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 28/46 (60%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL 63
          +  L+++TT + LR  F + GEV +  + RD  T+ SRGF FV  +
Sbjct: 5  IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 50

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 28/45 (62%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 28/45 (62%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 28/45 (62%)
Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 59

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 27/43 (62%)
Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L++ T    L +VF + G++ ++ + +DR T+ SRGF FV
Sbjct: 17 VGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFV 59

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 30/54 (55%)
Query: 7  PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          P   E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV
Sbjct: 5  PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 58

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	65
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	8e-25
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-22
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	9e-22
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-21
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-19
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-19
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-19
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	6e-18
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-16
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-16
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	8e-16
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-15
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-15
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-15
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-15
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	7e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-14
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-14
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-14
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-14
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-14
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-14
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	7e-14
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-13
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-13
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-13
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-13
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-13
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	7e-13
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	7e-13
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	8e-13
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	8e-13
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-05
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-12
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-12
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-12
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-12
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-12
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	5e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	9e-12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	7e-12
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-11
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-11
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-11
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-08
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	3e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-08
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-10
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-11
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-11
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-11
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-11
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-11
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	8e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	9e-11
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	9e-11
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-10
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-10
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-10
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-10
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-10
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-10
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-10
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-10
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-10
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-10
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-10
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	4e-10
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-10
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-08
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	7e-10
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	7e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	7e-10
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-10
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-04
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-09
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-09
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-09
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-09
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-09
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-09
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-09
2div_A	99	TRNA selenocysteine associated protein; structural	2e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-09
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-09
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-09
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-08
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-07
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-09
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-07
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-05
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-08
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-08
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-08
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	7e-08
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	9e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-07
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-07
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-07
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-07
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-07
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-07
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	6e-07
2dis_A	109	Unnamed protein product; structural genomics, RRM	7e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-06
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-06
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-06
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-06
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-06
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-06
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-06
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	4e-06
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	5e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	6e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-06
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	7e-06
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-06
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	8e-06
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	9e-06
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-05
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-05
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-05
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	6e-05
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	7e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-04
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-04
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-04
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	7e-04

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 87.3 bits (217), Expect = 8e-25
 Identities = 39/60 (65%), Positives = 48/60 (80%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          S G   P ++GM++LKVDNLTYRT+PD LRRVFE+ G VGD+YIPR+  T+  RGFAFVR
Sbjct: 2  SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 82.1 bits (203), Expect = 2e-22
 Identities = 50/61 (81%), Positives = 56/61 (91%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MSYGRPPP +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFV
Sbjct: 35 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94

Query: 61 R 61
          R
Sbjct: 95 R 95

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 81.0 bits (200), Expect = 9e-22
 Identities = 42/60 (70%), Positives = 49/60 (81%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
            +      +EGM SLKVDNLTYRT+PD LRRVFE+ G VGD+YIPRDR+T+ESRGFAFVR
Sbjct: 59  HHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 118

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 78.4 bits (194), Expect = 2e-21
 Identities = 19/58 (32%), Positives = 33/58 (56%)

Query: 4  GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
            P  R +   +++V NL+  T   DL+ +F   G +  IY+ +D+ T +S+GFAF+ 
Sbjct: 6  SGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFIS 63

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 74.8 bits (184), Expect = 1e-19
 Identities = 22/61 (36%), Positives = 30/61 (49%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
            +       +    L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV
Sbjct: 34 SRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93

Query: 61 R 61
           
Sbjct: 94 Y 94

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 73.4 bits (181), Expect = 2e-19
 Identities = 22/58 (37%), Positives = 29/58 (50%)

Query: 4  GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
                 +    L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV 
Sbjct: 6  SGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 63

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 72.2 bits (178), Expect = 6e-19
 Identities = 18/55 (32%), Positives = 31/55 (56%)

Query: 7  PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
               G   L V NL+Y ++ +DL ++F   G + +++ P D  T++ +GFAFV 
Sbjct: 2  SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVT 56

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 69.2 bits (170), Expect = 6e-18
 Identities = 22/60 (36%), Positives = 36/60 (60%), Gaps = 4/60 (6%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MS G  P +     ++ V NL +  T +DL R+F + G+V  + I +D+ TR+S+G AF+
Sbjct: 8  MSGGLAPSK----STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFI 63

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 65.6 bits (161), Expect = 1e-16
 Identities = 16/46 (34%), Positives = 26/46 (56%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          S+ V N+ Y  T ++L   F  CG V  + I  D+F+   +GFA++
Sbjct: 8  SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYI 53

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 66.6 bits (163), Expect = 2e-16
 Identities = 15/58 (25%), Positives = 24/58 (41%)

Query: 4  GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
             P R      L V  +    T +D+   F   GE+ +I++  DR T   +G+  V 
Sbjct: 13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 64.7 bits (158), Expect = 8e-16
 Identities = 16/46 (34%), Positives = 26/46 (56%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          S+ V N+ Y +T  DL   F  CG +  I I  D+F+   +G+A++
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYI 83

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 63.1 bits (154), Expect = 3e-15
 Identities = 17/43 (39%), Positives = 22/43 (51%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             L  R  P DL   F   G+V D+ I  DR +R S+G A+V
Sbjct: 30 CMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 72

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 64.1 bits (156), Expect = 3e-15
 Identities = 14/59 (23%), Positives = 29/59 (49%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
                  ++   +L V NL++ TT + +  +F + G++  I +  D+  + + GF FV
Sbjct: 28 DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFV 86

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 62.7 bits (153), Expect = 3e-15
 Identities = 15/60 (25%), Positives = 29/60 (48%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          S G    +    + L +  +       DL+ +FE  G++ ++ + +DRFT   +G AF+ 
Sbjct: 2  SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 63.3 bits (154), Expect = 5e-15
 Identities = 19/59 (32%), Positives = 22/59 (37%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             G           L V  L        L   F   G++ DI IP D  T + RGFAFV
Sbjct: 52  GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 110

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 61.9 bits (151), Expect = 7e-15
 Identities = 17/56 (30%), Positives = 26/56 (46%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
                 G + L V +L +  T D LR +FE  G +  I +  D  T  S+G+ F+
Sbjct: 18 NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFI 73

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 61.3 bits (149), Expect = 2e-14
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 5/58 (8%)

Query: 4  GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          G+ P +      +    L        L+ +  + GEV ++ I     TR+  G A V 
Sbjct: 2  GQIPLK-----EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVL 54

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 60.7 bits (148), Expect = 2e-14
 Identities = 14/55 (25%), Positives = 27/55 (49%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          P        ++ V  L  + +   L  +F + G V + ++P+DR T + +G+ FV
Sbjct: 8  PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFV 62

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 59.9 bits (146), Expect = 3e-14
 Identities = 16/48 (33%), Positives = 30/48 (62%)

Query: 13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          M ++ V NL Y  T + ++ +F + G+V ++ +  DR T++ +GF FV
Sbjct: 1  MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFV 48

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 60.0 bits (146), Expect = 3e-14
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVR 61
          ++ + N+   T  D +           V +I + +D+ T+++RGFAFV+
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQ 59

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 60.0 bits (146), Expect = 3e-14
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          S G  P + E   ++ V NL  R   + L  +F + G +  + I +DR  +  + F FV
Sbjct: 5  SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK-PKSFGFV 62

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 59.5 bits (145), Expect = 4e-14
 Identities = 17/43 (39%), Positives = 20/43 (46%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L        L   F   G++ DI IP D  T + RGFAFV
Sbjct: 12 VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 54

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 59.2 bits (144), Expect = 7e-14
 Identities = 17/43 (39%), Positives = 20/43 (46%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L        L   F   G++ DI IP D  T + RGFAFV
Sbjct: 17 VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 59

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 58.7 bits (143), Expect = 1e-13
 Identities = 15/43 (34%), Positives = 26/43 (60%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V +L +  T D LR +FE  G++ +I + +D  T  S+G+ F+
Sbjct: 10 VGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFI 52

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 59.4 bits (144), Expect = 2e-13
 Identities = 19/56 (33%), Positives = 31/56 (55%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +  P  + + +L V+ +        LR++FER G +  + I  DR TR+SRG+ FV
Sbjct: 34 QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFV 89

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 58.5 bits (142), Expect = 2e-13
 Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 7  PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-FTRESRGFAFV 60
           P+ +    + V N+ ++    ++R +F   GE+  + +P+    T   RGF FV
Sbjct: 9  VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 63

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 57.9 bits (141), Expect = 2e-13
 Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRF-TRESRGFAFV 60
          +  LT   T D +  +F   G++  I +P +R     S+G+A+V
Sbjct: 9  IGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYV 52

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 58.1 bits (141), Expect = 2e-13
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          P   +EG   L V ++      D+++  F   GE+ +I++  DR T  S+G+A V
Sbjct: 20 PQRSVEGW-ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 73

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 57.6 bits (140), Expect = 3e-13
 Identities = 16/43 (37%), Positives = 27/43 (62%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L++ T    L +VF + G++ ++ + +DR T+ SRGF FV
Sbjct: 17 VGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFV 59

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 58.1 bits (141), Expect = 3e-13
 Identities = 15/43 (34%), Positives = 19/43 (44%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          + NL+ R T  DL  +F R  E     I     T   RG AF+
Sbjct: 30 LKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFI 72

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 56.9 bits (138), Expect = 7e-13
 Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 6/57 (10%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
                     L V NL    T +++R++FE+ G+ G+++I +D      +GF F+R
Sbjct: 7  GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIR 57

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 56.9 bits (138), Expect = 7e-13
 Identities = 15/54 (27%), Positives = 25/54 (46%)

Query: 7  PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          P     + S+ V N+ Y  T + L+ +F   G V    +  DR T + +G+ F 
Sbjct: 2  PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFC 55

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 58.3 bits (141), Expect = 8e-13
 Identities = 16/57 (28%), Positives = 27/57 (47%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
              P R      L V ++      D+++  F   GE+ +I++  DR T  S+G+A V
Sbjct: 63  EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 119

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 57.0 bits (138), Expect = 8e-13
 Identities = 11/56 (19%), Positives = 26/56 (46%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
            P  +    ++ + NL++ +  + L  V ++ G++  + +     T  S+G AF 
Sbjct: 7  GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 62

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 58.1 bits (141), Expect = 2e-12
 Identities = 19/60 (31%), Positives = 25/60 (41%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +    P      M SL V +L    T   L   F   G +  I + RD  TR S G+A+V
Sbjct: 3  LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 38.8 bits (91), Expect = 2e-05
 Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 2/61 (3%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
            S   P  R  G+ ++ + NL        L   F   G +    +  D     S+G+ FV
Sbjct: 91  WSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFV 148

Query: 61  R 61
            
Sbjct: 149 H 149

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 54.8 bits (133), Expect = 3e-12
 Identities = 11/43 (25%), Positives = 21/43 (48%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +  L   TT  DL ++ +  G++       D+ T + +G+ FV
Sbjct: 10 IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFV 52

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 55.8 bits (135), Expect = 3e-12
 Identities = 13/58 (22%), Positives = 25/58 (43%)

Query: 4  GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
                      + V +L+   T +D++  F   G + D  + +D  T +S+G+ FV 
Sbjct: 6  SGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 54.4 bits (132), Expect = 3e-12
 Identities = 16/43 (37%), Positives = 22/43 (51%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L+  T  + +R  F   GEV  I +P D  T + RGF F+
Sbjct: 4  VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFI 46

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 55.3 bits (134), Expect = 3e-12
 Identities = 12/43 (27%), Positives = 21/43 (48%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  +    T +D+   F   GE+ +I++  DR T   +G+  V
Sbjct: 28 VTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 70

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 54.9 bits (133), Expect = 3e-12
 Identities = 10/43 (23%), Positives = 22/43 (51%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          + ++ Y  T + +  +    G V ++ +  D  T  S+G+AF+
Sbjct: 7  LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFI 49

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 55.0 bits (133), Expect = 4e-12
 Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 2/56 (3%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          R    +E    L +  L +  T ++L  + +  G V D+ +  +R   + +G A+V
Sbjct: 10 RYSTSLEKH-KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYV 63

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 54.5 bits (132), Expect = 4e-12
 Identities = 11/43 (25%), Positives = 21/43 (48%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  + +     +LR  F++ G V ++ +  D   +  RGF F+
Sbjct: 15 VGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFI 57

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 55.0 bits (133), Expect = 5e-12
 Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 1/45 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L +  L   T    L+ VF + G + ++ + +DR T +SRGFAF+
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFI 53

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 55.6 bits (135), Expect = 7e-12
 Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 2/58 (3%)

Query: 5   RPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           R  PR E   + K  V  +     P +    F + G + D  +  D+ T +SRGF FV
Sbjct: 77  RAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFV 134

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 55.2 bits (134), Expect = 9e-12
 Identities = 18/44 (40%), Positives = 25/44 (56%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          +  L + TT D+LR  F + G V D+ I +D  T  SRGF F+ 
Sbjct: 8  IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLS 51

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 53.7 bits (130), Expect = 7e-12
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 2/49 (4%)

Query: 14 VSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFV 60
          ++L + NLT+ TT +DL       G  ++ +I    +R   +S+GFA V
Sbjct: 2  IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 50

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 55.0 bits (133), Expect = 2e-11
 Identities = 23/61 (37%), Positives = 32/61 (52%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          MS    P   E +  L +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV
Sbjct: 1  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

Query: 61 R 61
           
Sbjct: 61 T 61

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 53.8 bits (130), Expect = 5e-11
 Identities = 17/43 (39%), Positives = 23/43 (53%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           V  +   T    LR  FE+ G++  I I  DR + + RGFAFV
Sbjct: 109 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 151

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 53.4 bits (129), Expect = 2e-11
 Identities = 18/44 (40%), Positives = 25/44 (56%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          V  L ++TT  DL+  F   GEV  + + +D  T  S+GF FVR
Sbjct: 20 VLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVR 63

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 52.5 bits (127), Expect = 2e-11
 Identities = 17/43 (39%), Positives = 25/43 (58%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L+  TT +D++  FE+ G+V D  +  D+ T   RGF FV
Sbjct: 4  VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFV 46

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 52.5 bits (127), Expect = 2e-11
 Identities = 12/44 (27%), Positives = 18/44 (40%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          V +L      + LR  F+        ++  D  T  SRG+ FV 
Sbjct: 6  VGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVS 49

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 54.5 bits (132), Expect = 2e-11
 Identities = 15/46 (32%), Positives = 25/46 (54%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +L V+ L    T ++ R +F   GE+    + RD+ T +S G+ FV
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFV 49

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 47.2 bits (113), Expect = 1e-08
 Identities = 19/60 (31%), Positives = 27/60 (45%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           SY RP        +L V  L    T  +L ++F + G +    I  D+ T  SRG  F+R
Sbjct: 77  SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIR 136

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 54.7 bits (131), Expect = 3e-11
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 4   GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFV 60
                     ++L + NLT+ TT +DL       G  ++ +I    +R   +S+GFA V
Sbjct: 59  NVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 117

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 54.6 bits (132), Expect = 3e-11
 Identities = 15/56 (26%), Positives = 26/56 (46%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +    +  M  + V ++ Y    D +R+ F   G +  I +  D  T + +GFAFV
Sbjct: 20 QRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 45.8 bits (109), Expect = 6e-08
 Identities = 12/43 (27%), Positives = 24/43 (55%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           V ++    + DD++ VFE  G++    + RD  T + +G+ F+
Sbjct: 130 VASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFI 172

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 53.7 bits (130), Expect = 4e-11
 Identities = 16/46 (34%), Positives = 22/46 (47%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +L V+ L    T  +L  +F   G +    I RD  T  S G+AFV
Sbjct: 5  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFV 50

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 50.6 bits (122), Expect = 5e-10
 Identities = 23/60 (38%), Positives = 28/60 (46%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           SY RP        +L V NL    T D L  +F + G +    I RD+ T   RG AFVR
Sbjct: 78  SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 137

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 52.3 bits (126), Expect = 4e-11
 Identities = 19/61 (31%), Positives = 23/61 (37%), Gaps = 5/61 (8%)

Query: 2  SYGRPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
          S G   P      S    V  L+  TT + L+  F          I  DR T  S+GF F
Sbjct: 2  SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGF 58

Query: 60 V 60
          V
Sbjct: 59 V 59

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 51.9 bits (125), Expect = 4e-11
 Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 6/50 (12%)

Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           GM  L + NL+   T DDLR++F          +P         G+AFV
Sbjct: 6  SGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFV 49

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 52.3 bits (126), Expect = 5e-11
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 3/60 (5%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           S G    +      L V N+ +R    DLR++F + G++ D+ I  +   R S+GF FV
Sbjct: 4  GSSGNSESKSTPK-RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFV 60

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 52.3 bits (126), Expect = 5e-11
 Identities = 18/43 (41%), Positives = 25/43 (58%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L Y TT   LR+ FE  G++ +  +  DR T +SRG+ FV
Sbjct: 22 VGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFV 64

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 52.3 bits (126), Expect = 5e-11
 Identities = 18/40 (45%), Positives = 26/40 (65%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L+++TT + LR  F + GEV +  + RD  T+ SRGF FV
Sbjct: 33 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 72

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 51.9 bits (125), Expect = 7e-11
 Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 3/62 (4%)

Query: 2  SYGRPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
          S G       G    K  V  L  + + +D+ R+F+  G + +  + R      S+G AF
Sbjct: 2  SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAF 60

Query: 60 VR 61
          V+
Sbjct: 61 VK 62

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 51.6 bits (124), Expect = 8e-11
 Identities = 15/56 (26%), Positives = 20/56 (35%), Gaps = 3/56 (5%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             P       + V NL       D+  VF + G + DI +      R    FAFV
Sbjct: 14 IRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFV 66

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 51.5 bits (124), Expect = 9e-11
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 3/59 (5%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          S+     + +    L V N+ +R    DLR++F + G++ D+ I  +   R S+GF FV
Sbjct: 19 SHMNTENKSQPK-RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFV 74

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 51.0 bits (123), Expect = 9e-11
 Identities = 12/44 (27%), Positives = 21/44 (47%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          V +L+   T   +   F   G + D  + +D  T +S+G+ FV 
Sbjct: 11 VGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVS 54

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 50.6 bits (122), Expect = 1e-10
 Identities = 17/40 (42%), Positives = 23/40 (57%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L++ T+  DL+  F + GEV D  I  D  T  SRGF F+
Sbjct: 19 LSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFI 58

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 51.1 bits (123), Expect = 1e-10
 Identities = 10/56 (17%), Positives = 19/56 (33%), Gaps = 1/56 (1%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
                   +L + NL    +  +L+          D+ +  D  T  +R F +V 
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVD 64

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 50.9 bits (122), Expect = 1e-10
 Identities = 11/44 (25%), Positives = 21/44 (47%)

Query: 17 KVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           + +         L  +F + G+V ++  P D  T +++GF FV
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 50.8 bits (122), Expect = 2e-10
 Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 6/44 (13%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          + N+ +  T  DL  +F+  G + D     +      +G  F++
Sbjct: 32 IGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIK 69

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 50.7 bits (122), Expect = 2e-10
 Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  +  R    ++R  F R G V ++ I  DR T  S+G+ FV
Sbjct: 14 VGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFV 55

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 50.7 bits (122), Expect = 2e-10
 Identities = 9/46 (19%), Positives = 19/46 (41%), Gaps = 2/46 (4%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +L V NL+   T   + ++F + G      +  +  +     + FV
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFV 60

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 51.8 bits (124), Expect = 2e-10
 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 2/45 (4%)

Query: 18  VDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFV 60
           V + ++ TT   L +V    G  +V ++    +R   +S+G+A V
Sbjct: 60  VGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEV 104

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 50.7 bits (122), Expect = 2e-10
 Identities = 19/40 (47%), Positives = 25/40 (62%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L + TT + LR  F + GEV D  I +D+ T +SRGF FV
Sbjct: 24 LDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 50.3 bits (121), Expect = 2e-10
 Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 5/56 (8%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
              ++    +L   NL++  T D+L+ VFE   E+            +S+G A++
Sbjct: 8  CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYI 58

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 49.8 bits (120), Expect = 2e-10
 Identities = 18/40 (45%), Positives = 26/40 (65%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L+++TT + LR  F + GEV +  + RD  T+ SRGF FV
Sbjct: 8  LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 47

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 49.9 bits (120), Expect = 3e-10
 Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE---SRGFAFV 60
          G   L + NL + TT + L+ VF + G +    I + +       S GF FV
Sbjct: 4  GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFV 55

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 50.4 bits (121), Expect = 4e-10
 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
               +E    L V NL +  +  D++ +F   G +    +  DR  R S G A V
Sbjct: 27 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADV 81

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 50.0 bits (120), Expect = 4e-10
 Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 2/61 (3%)

Query: 2  SYGRPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
          S G    + EG       + +L       DL ++F   G V    +  D+ T  S+ F F
Sbjct: 12 SIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGF 71

Query: 60 V 60
          V
Sbjct: 72 V 72

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 50.7 bits (122), Expect = 7e-10
 Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 2/45 (4%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE--SRGFAFV 60
          V  +    +  DLR +FE+ G V +I + RDR      S+G  FV
Sbjct: 8  VGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFV 52

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 45.7 bits (109), Expect = 4e-08
 Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           +  ++ + T +D+R +F   G++ +  I R      SRG AFV 
Sbjct: 100 IGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVT 142

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 49.3 bits (118), Expect = 7e-10
 Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 5/56 (8%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          R PP +     L + NL Y+ T +++  +F + G +  I +     T E+RG A+V
Sbjct: 2  RLPPEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYV 52

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 49.6 bits (119), Expect = 7e-10
 Identities = 16/41 (39%), Positives = 26/41 (63%)

Query: 21 LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          L++ TT + LR  +E+ G++ D  + RD  ++ SRGF FV 
Sbjct: 35 LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 75

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 49.2 bits (118), Expect = 7e-10
 Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 8/51 (15%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGD--------IYIPRDRFTRESRGFAFV 60
          V  L    T + +   F++ G +          I +  DR T + +G A V
Sbjct: 18 VQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 68

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 51.1 bits (123), Expect = 8e-10
 Identities = 10/46 (21%), Positives = 17/46 (36%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           L V NL    T      +    G +   ++     T +S+G+ F  
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAE 143

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 42.3 bits (100), Expect = 1e-06
 Identities = 10/47 (21%), Positives = 15/47 (31%), Gaps = 2/47 (4%)

Query: 16  LKVDNLTYRTT-PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           L VD L       D L R            +   +  +  +GFA + 
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQ-LKGFAVLE 232

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 35.3 bits (82), Expect = 3e-04
 Identities = 8/45 (17%), Positives = 15/45 (33%), Gaps = 7/45 (15%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
          +  L    T  ++  +             +  F  + +G AFV L
Sbjct: 27 IRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTL 64

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 48.9 bits (117), Expect = 1e-09
 Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 8/51 (15%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEV--------GDIYIPRDRFTRESRGFAFV 60
          V  L    T + +   F++ G +          I +  DR T + +G A V
Sbjct: 12 VQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 48.8 bits (117), Expect = 1e-09
 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
               +E    L V NL +  +  D++ +F   G +    +  DR  R S G A V
Sbjct: 21 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADV 75

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 48.0 bits (115), Expect = 1e-09
 Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 5/43 (11%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V   T   T ++L++ F + GEV D++IP+       R FAFV
Sbjct: 16 VGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFV 53

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 48.6 bits (116), Expect = 2e-09
 Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 8/51 (15%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEV--------GDIYIPRDRFTRESRGFAFV 60
          V  L    T DDL   F++CG V          I+I  D+ T + +G A V
Sbjct: 20 VQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 47.6 bits (114), Expect = 2e-09
 Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 5/43 (11%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V   T   T D+LR  F + G+V D++IP+       R FAFV
Sbjct: 10 VGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFV 47

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 48.3 bits (115), Expect = 2e-09
 Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 6/49 (12%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLL 63
           +   NL   T   +++  F R G +G + +P      E    A V  L
Sbjct: 12 VILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFL 54

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 48.0 bits (115), Expect = 2e-09
 Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
                E   +  V NL + T   D+  +F+    +  + + RD+ T + +GF +V
Sbjct: 7  GKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYV 61

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 48.1 bits (115), Expect = 2e-09
 Identities = 13/43 (30%), Positives = 18/43 (41%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          + +L    T  DL   F   G V    +  D+ T  S+ F FV
Sbjct: 45 IYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFV 87

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 47.7 bits (114), Expect = 2e-09
 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIPRDRFTRESRGFAFV 60
          SL + +L      + + R F   GE V  + I R+R T    G+ FV
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFV 57

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 48.7 bits (116), Expect = 2e-09
 Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 5/48 (10%)

Query: 13  MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
              + V NL       +L R F   G +  +++ R+       GFAFV
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFV 115

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 47.6 bits (114), Expect = 3e-09
 Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 7/58 (12%)

Query: 7  PPRIEGMVSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFV 60
           P      ++ ++NL  +   D+L++    +F R G++ DI + R   + + RG AFV
Sbjct: 2  VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFV 56

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 47.7 bits (114), Expect = 3e-09
 Identities = 9/44 (20%), Positives = 20/44 (45%), Gaps = 6/44 (13%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
             +    T   +R+ F   G++ +I +  +      +G++FVR
Sbjct: 30 CGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVR 67

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 47.7 bits (114), Expect = 3e-09
 Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 5/47 (10%)

Query: 14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          + + V NL       +L R F   G +  ++I R+       GFAFV
Sbjct: 1  MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFV 42

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 48.8 bits (117), Expect = 3e-09
 Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 1/59 (1%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          S+           +L + NL    +  +L+          D+ +   R T  +R F +V
Sbjct: 2  SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYV 59

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 43.0 bits (102), Expect = 5e-07
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 5/59 (8%)

Query: 2   SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             GR   ++    +L   NL++  T D+L+ VFE   E     I       +S+G A++
Sbjct: 88  PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYI 141

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 49.2 bits (118), Expect = 5e-09
 Identities = 9/57 (15%), Positives = 23/57 (40%), Gaps = 2/57 (3%)

Query: 4  GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
               R   + ++ V NL      + + + F+ CG +  + +      +++  FA +
Sbjct: 32 NEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARI 86

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 46.1 bits (110), Expect = 5e-08
 Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 2/44 (4%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFV 60
           + N     T  ++R + +    V   I +P  RF   SR FA++
Sbjct: 122 MTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNT-SRRFAYI 164

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 43.1 bits (102), Expect = 6e-07
 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 14  VSLKVDNLTYRTTPDD-LRRVFERCGEVGDIYIPRDRF-TRESRGFAFVR 61
             + + NL+     ++ LR  FE  G +  I IP  +     +   AF+ 
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMV 260

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 47.9 bits (115), Expect = 5e-09
 Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           L V NL    T D L++ F+  G + +I I  D+   ++  +AFV
Sbjct: 2  VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFV 46

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 43.3 bits (103), Expect = 3e-07
 Identities = 13/61 (21%), Positives = 23/61 (37%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
            ++       +   +L V +L      + LR  F+        ++  D  T  SRG+ FV
Sbjct: 75  WAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFV 134

Query: 61  R 61
            
Sbjct: 135 S 135

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 46.9 bits (112), Expect = 5e-09
 Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 4/46 (8%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +L + NL+Y  T + L+ VFE+   +  +         +S+G+AF+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFI-KVP---QNQNGKSKGYAFI 58

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 48.9 bits (117), Expect = 6e-09
 Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 6/57 (10%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
                     L V NL    T +D +R+FER GE  +++I RD      RGF F+R
Sbjct: 14 PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIR 64

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 37.7 bits (88), Expect = 5e-05
 Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 1/46 (2%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           L V NL+   + + L + F + G V    +  D   R + G  FV 
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGR-ATGKGFVE 143

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 45.3 bits (108), Expect = 2e-08
 Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 10/60 (16%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          + YG+  P       L V  L   T+   L R F+R G +  I   +         FA++
Sbjct: 9  IGYGKANPTT----RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYI 58

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 45.5 bits (108), Expect = 2e-08
 Identities = 9/57 (15%), Positives = 19/57 (33%), Gaps = 2/57 (3%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFVR 61
                  V   + N+ +  T  D+ +  E        +++  D   +   G A V+
Sbjct: 8  EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQ-GLGQALVQ 63

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.7 bits (106), Expect = 4e-08
 Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +       T DD++   E  G+V +I + R    +  +G  FV
Sbjct: 16 IKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFV 57

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 46.0 bits (109), Expect = 4e-08
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
                +E    L V NL +  +  D++ +F   G +    +  DR +  S G A V
Sbjct: 80  GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADV 134

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 45.8 bits (109), Expect = 6e-08
 Identities = 9/43 (20%), Positives = 18/43 (41%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           +  L      D ++ +    G +    + +D  T  S+G+AF 
Sbjct: 119 IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 161

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 42.7 bits (101), Expect = 6e-07
 Identities = 8/48 (16%), Positives = 17/48 (35%), Gaps = 5/48 (10%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPR-----DRFTRESRGFAFV 60
          V N+ +  T + +   F     +G +              + + FAF+
Sbjct: 9  VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFL 56

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 44.4 bits (105), Expect = 7e-08
 Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 2/60 (3%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          S G+P P     + + V  + +    +D+R  F     V  +++ +D   R + G   V+
Sbjct: 5  SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGR-NNGNGLVK 62

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 44.5 bits (105), Expect = 8e-08
 Identities = 11/61 (18%), Positives = 25/61 (40%), Gaps = 7/61 (11%)

Query: 4  GRPPPRIEGMVSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAF 59
          G  PP  E    + + N+      + L+     +    G++ DI +     + ++ G A+
Sbjct: 20 GSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAY 76

Query: 60 V 60
          +
Sbjct: 77 I 77

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 44.9 bits (107), Expect = 9e-08
 Identities = 11/56 (19%), Positives = 21/56 (37%)

Query: 5   RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
                + G   L +  L      D ++ +    G +    + +D  T  S+G+AF 
Sbjct: 86  HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 141

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 42.6 bits (101), Expect = 6e-07
 Identities = 8/48 (16%), Positives = 17/48 (35%), Gaps = 5/48 (10%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPR-----DRFTRESRGFAFV 60
          V N+ +  T + +   F     +G +              + + FAF+
Sbjct: 9  VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFL 56

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 43.5 bits (103), Expect = 9e-08
 Identities = 11/50 (22%), Positives = 17/50 (34%), Gaps = 5/50 (10%)

Query: 11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           G+ S+ V           L   F   G V  + + +D+       FA V
Sbjct: 6  SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIV 50

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 45.2 bits (106), Expect = 1e-07
 Identities = 12/60 (20%), Positives = 21/60 (35%), Gaps = 1/60 (1%)

Query: 1   MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
                         S+ +       T DD++   E  G+V +I + R    +  +G  FV
Sbjct: 97  PEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFV 155

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 43.7 bits (104), Expect = 1e-07
 Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 2/43 (4%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V NL      + LR+ F   G +    +  +     S+GF FV
Sbjct: 20 VKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFV 60

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 43.0 bits (102), Expect = 1e-07
 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 6/47 (12%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          +L V  L    T  DLR  F + GE+  I + +       +  AF++
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQ 54

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 43.1 bits (102), Expect = 1e-07
 Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 5/60 (8%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          S G+P P +     +KV N+ +  + D++   F     +      +        G A V 
Sbjct: 9  SSGKPGPTV-----IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 43.5 bits (103), Expect = 1e-07
 Identities = 18/61 (29%), Positives = 23/61 (37%), Gaps = 3/61 (4%)

Query: 2  SYGRPPPRIEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
          S G       G +     V NL Y+     L+ VF   G V    I  D+  + SRG   
Sbjct: 2  SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGK-SRGIGT 60

Query: 60 V 60
          V
Sbjct: 61 V 61

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 43.0 bits (102), Expect = 2e-07
 Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          + NL       +L  + +  G+V    I RD  +  SRG  F R
Sbjct: 30 ISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFAR 72

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 42.3 bits (100), Expect = 3e-07
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 7/61 (11%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFV 60
          S G+P P I     +KV N+ +  + D++   F     + G + +  +       G A V
Sbjct: 9  SSGKPGPTI-----IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGM-PTGEAMV 62

Query: 61 R 61
           
Sbjct: 63 A 63

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 41.8 bits (99), Expect = 4e-07
 Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 2/53 (3%)

Query: 8  PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
              G   + V NL +  T   L+  F  CG V    I  +    +S+G   V
Sbjct: 3  SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVV 53

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 41.4 bits (98), Expect = 5e-07
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 8/49 (16%)

Query: 12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          GMV L + NL    T  ++R +FE+ G+V +  I         + + FV
Sbjct: 7  GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFV 47

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 41.8 bits (99), Expect = 5e-07
 Identities = 10/47 (21%), Positives = 21/47 (44%), Gaps = 2/47 (4%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE-SRGFAFV 60
          +  + NL Y  T + ++  F     +  + +PR+    E  +GF + 
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYA 66

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 41.9 bits (99), Expect = 6e-07
 Identities = 13/60 (21%), Positives = 25/60 (41%), Gaps = 3/60 (5%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE-SRGFAFV 60
          S G   P+     +  + NL Y  T + ++  F     +  + +PR+    E  +GF + 
Sbjct: 5  SSGSRLPK-SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYA 62

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 41.7 bits (98), Expect = 7e-07
 Identities = 9/45 (20%), Positives = 19/45 (42%), Gaps = 2/45 (4%)

Query: 18 VDNLTYRTTPDDLRRVFERCGE-VGDIYIPRD-RFTRESRGFAFV 60
          +  +      +++     +  E V D+ +        ++RGFAFV
Sbjct: 13 IGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFV 57

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 42.5 bits (99), Expect = 1e-06
 Identities = 17/55 (30%), Positives = 29/55 (52%)

Query: 6   PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           P  + +   +L V  + Y TT   LRR FE  G +  I++   + + + RG+AF+
Sbjct: 95  PNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 40.6 bits (96), Expect = 1e-06
 Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 1/45 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGD-IYIPRDRFTRESRGFAFVR 61
          + NL        L   F   G +     I RD  T  S+G+AF+ 
Sbjct: 10 IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFIN 54

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 40.7 bits (96), Expect = 1e-06
 Identities = 9/43 (20%), Positives = 16/43 (37%), Gaps = 6/43 (13%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V NL   T+ + + + F          + +       R +AFV
Sbjct: 20 VRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFV 56

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 41.1 bits (97), Expect = 1e-06
 Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 2/43 (4%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          + NL        L   F   G +    +  D     S+G+ FV
Sbjct: 10 IKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFV 50

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 42.0 bits (98), Expect = 1e-06
 Identities = 4/43 (9%), Positives = 10/43 (23%)

Query: 18  VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
             N     T ++   + +  G      +       E      +
Sbjct: 128 FFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLL 170

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 35.1 bits (80), Expect = 4e-04
 Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 6/46 (13%)

Query: 18 VDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
          V  L   +   D +  VF   G V  +   + +      G A V +
Sbjct: 9  VYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEM 49

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 40.7 bits (96), Expect = 2e-06
 Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 8/43 (18%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V          +L  +F   G + ++ I          GFAFV
Sbjct: 36 VRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFV 70

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 41.0 bits (96), Expect = 2e-06
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 2/63 (3%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAF 59
          M  G           +++  L +  T +++ + F     V   I +P D   +   G AF
Sbjct: 30 MGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK-ITGEAF 88

Query: 60 VRL 62
          V+ 
Sbjct: 89 VQF 91

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 41.0 bits (96), Expect = 2e-06
 Identities = 11/62 (17%), Positives = 19/62 (30%), Gaps = 2/62 (3%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAF 59
              R     E    + +  L +      +   F++   V   IYI      + + G  F
Sbjct: 13 QKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK-ATGEGF 71

Query: 60 VR 61
          V 
Sbjct: 72 VE 73

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 39.5 bits (93), Expect = 3e-06
 Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 8/43 (18%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V N++   T  +LR +FER G V +  +         + +AFV
Sbjct: 14 VGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFV 48

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 39.7 bits (93), Expect = 3e-06
 Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 2/56 (3%)

Query: 8  PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFVRL 62
          P       +++  L +  + +++ + F     V   + +P D   R S G AFV+ 
Sbjct: 10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR-STGEAFVQF 64

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 39.9 bits (93), Expect = 4e-06
 Identities = 11/62 (17%), Positives = 20/62 (32%), Gaps = 5/62 (8%)

Query: 4  GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD----IYIPRDRFTRESRGFAF 59
                 E  V +++  L +  T +++   F +   +      I        R   G AF
Sbjct: 14 VAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR-PTGDAF 72

Query: 60 VR 61
          V 
Sbjct: 73 VL 74

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 39.8 bits (93), Expect = 5e-06
 Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 5/48 (10%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEV-----GDIYIPRDRFTRESRGFAFV 60
          V NL       DL+ +F R  +        ++  R       +G AF+
Sbjct: 50 VKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFI 97

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 38.9 bits (91), Expect = 6e-06
 Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 2/46 (4%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          + +  L YR T +D+   F     +  ++I      R   G A V 
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGR-VTGEADVE 61

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 40.2 bits (93), Expect = 7e-06
 Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 7/59 (11%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFV 60
            P      ++ ++NL  +   D+L++    +F + G++ DI + R   + + RG AFV
Sbjct: 2  AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFV 57

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 38.5 bits (90), Expect = 7e-06
 Identities = 6/44 (13%), Positives = 22/44 (50%), Gaps = 2/44 (4%)

Query: 17 KVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +V         + + ++F + G++ + + P +    +++G+ F+
Sbjct: 11 QVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFL 52

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 38.8 bits (91), Expect = 7e-06
 Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 8/43 (18%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V NL    T + L + F + G++  +   +D        +AF+
Sbjct: 16 VRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFI 50

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 38.4 bits (90), Expect = 8e-06
 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 8/43 (18%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V N++   T  +LR  FE  G V +  I         + +AFV
Sbjct: 15 VGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFV 49

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 39.1 bits (91), Expect = 9e-06
 Identities = 11/58 (18%), Positives = 19/58 (32%), Gaps = 2/58 (3%)

Query: 4  GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
               +      + +  L Y+ T +D+   F     V  ++I      R   G A V 
Sbjct: 37 SEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPDGR-VTGEADVE 92

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 38.3 bits (89), Expect = 2e-05
 Identities = 9/50 (18%), Positives = 19/50 (38%), Gaps = 6/50 (12%)

Query: 18 VDNLTYRTTPDDLRR---VFERCGEVGDIYIPRDRFTRESR---GFAFVR 61
          V  L+ R    ++ +    F + G++  + I        S+     A+V 
Sbjct: 20 VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVT 69

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 38.0 bits (88), Expect = 2e-05
 Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 6/42 (14%)

Query: 20 NLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           L    + + L  V E+CG V  + +P +      + ++F R
Sbjct: 34 GLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFAR 69

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 38.0 bits (88), Expect = 2e-05
 Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 2/45 (4%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRD--RFTRESRGFAFV 60
          V  L      D++   F R G +   +  +   +     +G+AF+
Sbjct: 13 VGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFL 57

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 37.4 bits (87), Expect = 3e-05
 Identities = 6/44 (13%), Positives = 22/44 (50%), Gaps = 2/44 (4%)

Query: 17 KVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +V         + + ++F + G++ + + P +    +++G+ F+
Sbjct: 25 QVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFL 66

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 36.9 bits (86), Expect = 4e-05
 Identities = 11/37 (29%), Positives = 14/37 (37%), Gaps = 6/37 (16%)

Query: 25 TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
           TP  LR  F   G + D+ +         R  AFV 
Sbjct: 25 MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVT 55

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 36.7 bits (85), Expect = 6e-05
 Identities = 8/45 (17%), Positives = 13/45 (28%), Gaps = 6/45 (13%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
          V  L       DL    E+ G +  + +         +  A V  
Sbjct: 20 VRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEF 58

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 37.6 bits (87), Expect = 6e-05
 Identities = 10/47 (21%), Positives = 23/47 (48%), Gaps = 4/47 (8%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
           L + N+    + +DL+ +F   G V    +   +F ++ R  A +++
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQM 165

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 36.3 bits (84), Expect = 6e-05
 Identities = 6/52 (11%), Positives = 16/52 (30%)

Query: 8  PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
          P+ + +  L++ N+      + L  +  + G V                  +
Sbjct: 10 PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTY 61

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 36.9 bits (85), Expect = 7e-05
 Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 4/44 (9%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          V+NL Y  T D L ++F + G V  I      FT+ ++  A ++
Sbjct: 33 VENLFYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALLQ 72

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 36.9 bits (85), Expect = 1e-04
 Identities = 10/47 (21%), Positives = 23/47 (48%), Gaps = 4/47 (8%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
           L + N+    + +DL+ +F   G V    +   +F ++ R  A +++
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQM 196

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 36.1 bits (83), Expect = 2e-04
 Identities = 15/59 (25%), Positives = 21/59 (35%), Gaps = 6/59 (10%)

Query: 4  GRPPPRIEGMVSLKVDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
            P     G   L V NL   R TP  L  +F   G+V  +     +     +  A V+
Sbjct: 25 AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQ 78

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 35.2 bits (81), Expect = 2e-04
 Identities = 16/60 (26%), Positives = 20/60 (33%), Gaps = 8/60 (13%)

Query: 4  GRPPPRIEG---MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          G   P  EG      + V NL       DL+R     G V     P     +  R  AF+
Sbjct: 7  GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFL 61

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 34.7 bits (80), Expect = 2e-04
 Identities = 6/45 (13%), Positives = 12/45 (26%), Gaps = 6/45 (13%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
          +  L       DL    +  G +  + +         +  A V  
Sbjct: 26 IRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEF 64

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 35.5 bits (81), Expect = 3e-04
 Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 4/45 (8%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          + V+NL Y  T D L ++F + G V  I      FT+ ++  A +
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALL 89

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 34.4 bits (79), Expect = 4e-04
 Identities = 8/62 (12%), Positives = 22/62 (35%), Gaps = 11/62 (17%)

Query: 1  MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
                P R+     + +  L    T  ++  +    G+V ++ + +       +  AF+
Sbjct: 9  HHGSGVPSRV-----IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFI 57

Query: 61 RL 62
           +
Sbjct: 58 EM 59

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 33.4 bits (76), Expect = 7e-04
 Identities = 11/52 (21%), Positives = 24/52 (46%), Gaps = 7/52 (13%)

Query: 14 VSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVR 61
            ++V N+ YR +  +L++     F R G+V  + +       + +  A V+
Sbjct: 10 ADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPH---TDYQLKAVVQ 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	65
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.79
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.79
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.78
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.77
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.77
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.76
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.76
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.75
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.75
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.75
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.75
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.75
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.75
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.75
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.74
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.74
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.74
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.74
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.73
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.73
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.73
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.73
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.73
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.73
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.73
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.73
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.73
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.73
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.73
2div_A	99	TRNA selenocysteine associated protein; structural	99.72
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.72
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.72
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.72
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.72
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.72
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.72
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.72
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.72
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.72
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.72
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.72
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.71
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.71
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.71
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.71
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.71
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.71
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.71
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.7
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.7
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.7
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.7
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.7
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.7
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.7
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.7
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.7
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.7
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.7
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.7
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.7
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.7
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.69
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.69
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.69
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.68
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.68
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.68
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.68
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.68
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.68
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.68
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.68
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.68
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.67
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.67
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.67
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.67
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.67
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.67
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.67
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.67
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.67
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.67
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.66
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.66
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.66
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.66
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.66
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.66
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.66
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.66
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.66
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.66
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.66
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.66
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.66
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.65
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.65
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.64
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.64
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.63
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.62
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.62
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.62
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.62
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.62
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.62
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.61
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.61
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.61
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.61
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.6
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.59
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.59
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.59
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.59
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.59
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.59
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.59
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.58
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.58
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.58
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.58
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.58
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.58
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.57
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.57
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.35
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.56
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.56
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.55
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.55
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.55
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.55
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.54
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.54
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.54
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.53
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.53
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.53
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.53
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.53
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.52
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.52
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.52
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.52
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.52
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.51
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.51
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.51
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.51
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.5
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.5
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.5
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.5
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.5
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.5
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.49
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.48
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.48
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.47
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.46
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.46
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.46
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.45
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.45
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.45
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.44
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.44
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.43
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.43
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.4
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.4
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.4
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.4
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.38
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.38
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.38
1x5p_A	97	Negative elongation factor E; structure genomics,	99.37
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.36
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.35
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.34
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.34
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.32
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.31
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.31
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.29
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.28
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.24
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.23
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.22
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.2
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.2
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.15
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.14
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.1
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.1
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.0
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.89
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.89
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.79
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.7
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.14
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	97.93
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.27
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	97.18
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.6
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.55
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	96.12
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	95.94
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.58
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	92.01
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	90.72

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.79  E-value=5.8e-19  Score=86.98  Aligned_cols=54  Identities=31%  Similarity=0.450  Sum_probs=50.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      -++++|||+|||+++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~   70 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVT   70 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECC
Confidence            345899999999999999999999999999999999999999999999999976

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=9e-19  Score=86.35  Aligned_cols=62  Identities=61%  Similarity=1.098  Sum_probs=57.5

Q ss_pred             CCCCCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           3 YGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         3 ~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++++++..+..++|||+|||+++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus         3 ~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   64 (103)
T 2dnm_A            3 SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD   64 (103)
T ss_dssp             CCCCSSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESS
T ss_pred             CCCCCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECC
Confidence            56677777888999999999999999999999999999999999998899999999999986

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.78  E-value=2.9e-18  Score=82.25  Aligned_cols=58  Identities=33%  Similarity=0.425  Sum_probs=52.5

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +......++|||+|||+++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus         5 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~   62 (87)
T 3s7r_A            5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD   62 (87)
T ss_dssp             --CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECC
Confidence            3455667899999999999999999999999999999999999899999999999986

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=5.5e-18  Score=83.00  Aligned_cols=59  Identities=19%  Similarity=0.281  Sum_probs=53.8

Q ss_pred             CCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         6 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.......++|||+|||.++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus         3 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   61 (99)
T 2dgs_A            3 SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED   61 (99)
T ss_dssp             CCCCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESS
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECC
Confidence            44455667999999999999999999999999999999999998899999999999975

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.77  E-value=2e-18  Score=92.27  Aligned_cols=64  Identities=36%  Similarity=0.544  Sum_probs=54.5

Q ss_pred             CCCCCCCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           1 MSYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         1 ~~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |+.+.++.+.+..++|||+|||+++++++|+++|..||.|..+.++.++.++.++|||||+|.+
T Consensus         1 ms~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~   64 (196)
T 1l3k_A            1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT   64 (196)
T ss_dssp             -------CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCcccCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCC
Confidence            6777778788888999999999999999999999999999999999999899999999999975

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.76  E-value=5.6e-18  Score=84.84  Aligned_cols=52  Identities=21%  Similarity=0.227  Sum_probs=50.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||+++++++|+++|+.||.|.++.++.++.+++++|||||+|.+
T Consensus         6 ~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~   57 (110)
T 3s8s_A            6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTS   57 (110)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECC
Confidence            4899999999999999999999999999999999999999999999999975

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.76  E-value=8.5e-18  Score=82.38  Aligned_cols=62  Identities=19%  Similarity=0.119  Sum_probs=55.4

Q ss_pred             CCCCCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEE--------EEEeecCCCCCcccEEEEEEee
Q psy7053           3 YGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD--------IYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         3 ~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~--------~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+.......+|||+|||+++++++|+++|+.+|.|..        +.++.++.+++++|||||+|.+
T Consensus         3 ~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~   72 (99)
T 2la6_A            3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD   72 (99)
T ss_dssp             SSCSCCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSS
T ss_pred             CCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECC
Confidence            3445556667799999999999999999999999999998        9999998899999999999975

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.5e-17  Score=81.96  Aligned_cols=57  Identities=33%  Similarity=0.480  Sum_probs=52.3

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......++|||+|||+.+++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~   66 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE   66 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESS
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECC
Confidence            344556899999999999999999999999999999999998899999999999975

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=1.1e-17  Score=82.69  Aligned_cols=58  Identities=36%  Similarity=0.525  Sum_probs=53.5

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +...+..++|||+|||+.+++++|+++|..||.|..+.++.++.++.++|||||+|.+
T Consensus        10 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~   67 (105)
T 2dh8_A           10 NSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD   67 (105)
T ss_dssp             CCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESS
T ss_pred             cCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECC
Confidence            3455667999999999999999999999999999999999998899999999999986

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.5e-17  Score=82.10  Aligned_cols=59  Identities=25%  Similarity=0.430  Sum_probs=53.7

Q ss_pred             CCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         6 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++......++|||+|||+.+++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   66 (105)
T 1x5u_A            8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS   66 (105)
T ss_dssp             CCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESS
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECC
Confidence            34455667999999999999999999999999999999999998899999999999976

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.75  E-value=7.9e-18  Score=83.24  Aligned_cols=59  Identities=22%  Similarity=0.399  Sum_probs=53.6

Q ss_pred             CCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         6 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++......++|||+|||..+++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus         6 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~   64 (106)
T 2dgp_A            6 SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE   64 (106)
T ss_dssp             CSCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESS
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECC
Confidence            34455666899999999999999999999999999999999998899999999999975

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.3e-17  Score=82.52  Aligned_cols=58  Identities=26%  Similarity=0.330  Sum_probs=52.7

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +......++|||+|||..+++++|+++|..||.|..+.++.++.++.++|||||+|.+
T Consensus        17 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   74 (106)
T 1p27_B           17 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET   74 (106)
T ss_dssp             BCCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECC
Confidence            3344556899999999999999999999999999999999999999999999999976

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.75  E-value=2.6e-18  Score=84.27  Aligned_cols=56  Identities=27%  Similarity=0.421  Sum_probs=50.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCC--EEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGE--VGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~--i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......+|||+|||+++++++|++.|++||.  +.+++++.++.+++++|||||+|.+
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~   62 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSS   62 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSS
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECC
Confidence            3455689999999999999999999999995  5688999999999999999999986

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.75  E-value=2.5e-18  Score=88.05  Aligned_cols=58  Identities=22%  Similarity=0.367  Sum_probs=52.0

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEE--EEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD--IYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~--~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +......++|||+|||+++++++|+++|..||.|..  ++++.++.+|+++|||||+|.+
T Consensus        17 ~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~   76 (131)
T 2m2b_A           17 PSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLST   76 (131)
T ss_dssp             CCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCH
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECC
Confidence            334455689999999999999999999999999966  8999999999999999999975

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=1.8e-17  Score=82.46  Aligned_cols=58  Identities=19%  Similarity=0.387  Sum_probs=53.1

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +......++|||+|||+++++++|+++|..||.|..+.++.++.++.++|||||+|.+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~   66 (111)
T 1x4h_A            9 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMT   66 (111)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESS
T ss_pred             CCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECC
Confidence            3455667899999999999999999999999999999999999999999999999975

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.2e-17  Score=82.88  Aligned_cols=55  Identities=22%  Similarity=0.225  Sum_probs=50.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|+.||.|..+.++.++. +.++|||||+|.+
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~   61 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDS   61 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESS
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECC
Confidence            344558999999999999999999999999999999999986 9999999999975

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3.2e-17  Score=82.24  Aligned_cols=58  Identities=31%  Similarity=0.508  Sum_probs=52.9

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +......++|||+|||+++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   68 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD   68 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESS
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECC
Confidence            3445566899999999999999999999999999999999998899999999999975

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=3e-17  Score=79.58  Aligned_cols=58  Identities=33%  Similarity=0.489  Sum_probs=52.8

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .......++|||+|||..+++++|+++|..+|.|..+.++.++.+++++|||||+|.+
T Consensus        10 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~   67 (94)
T 2e5h_A           10 GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLD   67 (94)
T ss_dssp             CSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESC
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECC
Confidence            3445566899999999999999999999999999999999998899999999999976

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.73  E-value=2.3e-17  Score=82.06  Aligned_cols=58  Identities=28%  Similarity=0.340  Sum_probs=52.8

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +......++|||+|||..+++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        20 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   77 (110)
T 1oo0_B           20 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET   77 (110)
T ss_dssp             BCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECC
Confidence            3445566899999999999999999999999999999999998899999999999976

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.73  E-value=4.6e-17  Score=81.50  Aligned_cols=58  Identities=22%  Similarity=0.415  Sum_probs=53.0

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.+....++|||+|||+.+++++|+++|..||.|..+.++.++.++.++|||||+|.+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   66 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN   66 (115)
T ss_dssp             CCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECC
Confidence            3455666899999999999999999999999999999999998899999999999975

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=2.3e-17  Score=81.27  Aligned_cols=59  Identities=32%  Similarity=0.631  Sum_probs=53.7

Q ss_pred             CCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         6 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +..+.+..++|||+|||.++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   66 (103)
T 2cq0_A            8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR   66 (103)
T ss_dssp             SCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESS
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECC
Confidence            34455667999999999999999999999999999999999998899999999999975

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.73  E-value=2.8e-18  Score=88.47  Aligned_cols=63  Identities=78%  Similarity=1.341  Sum_probs=57.3

Q ss_pred             CCCCCCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           2 SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         2 ~~~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +++.++++....++|||+|||+++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        36 ~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~   98 (135)
T 2lea_A           36 SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD   98 (135)
T ss_dssp             CSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSC
T ss_pred             CcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECC
Confidence            456667777778999999999999999999999999999999999998899999999999976

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.73  E-value=1.8e-18  Score=84.05  Aligned_cols=52  Identities=27%  Similarity=0.436  Sum_probs=48.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccC-CEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.+|||+|||+++++++|+++|+.+| .|..++++.++.+++++|||||+|.+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~   53 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSH   53 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecC
Confidence            36899999999999999999999999 79999999999999999999999976

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=3.8e-17  Score=79.29  Aligned_cols=57  Identities=39%  Similarity=0.513  Sum_probs=52.3

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+..++|||+|||..+++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~   66 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN   66 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESS
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECC
Confidence            344556899999999999999999999999999999999999899999999999976

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.73  E-value=1.6e-17  Score=82.88  Aligned_cols=56  Identities=32%  Similarity=0.540  Sum_probs=49.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+..++|||+|||+++++++|+++|..||.|..+.++.++.+|.++|||||+|.+
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~   76 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD   76 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECC
Confidence            44556899999999999999999999999999999999998899999999999975

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.73  E-value=4.7e-17  Score=81.78  Aligned_cols=56  Identities=25%  Similarity=0.167  Sum_probs=51.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +....++|||+|||+++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~   91 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDN   91 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECC
Confidence            34455899999999999999999999999999999999998899999999999986

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=2.7e-17  Score=78.54  Aligned_cols=54  Identities=24%  Similarity=0.345  Sum_probs=50.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+++++++|+++|..+|.|..+.++.++.++.++|||||+|.+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~   56 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDS   56 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECC
Confidence            345899999999999999999999999999999999998899999999999976

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.73  E-value=4.1e-17  Score=81.34  Aligned_cols=58  Identities=29%  Similarity=0.440  Sum_probs=53.1

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++.....++|||+|||..+++++|+++|+.||.|..+.++.++.++.++|||||+|.+
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~   77 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD   77 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESC
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECC
Confidence            4455666899999999999999999999999999999999998899999999999975

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=4.9e-17  Score=80.43  Aligned_cols=58  Identities=24%  Similarity=0.552  Sum_probs=52.5

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeec-CCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRD-RFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~g~~fv~f~~   64 (65)
                      +......++|||+|||+.+++++|+++|..||.|..+.++.+ +.+++++|||||+|.+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~   67 (107)
T 2cph_A            9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT   67 (107)
T ss_dssp             SCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESS
T ss_pred             cccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECC
Confidence            345556689999999999999999999999999999999988 7899999999999976

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.8e-17  Score=80.39  Aligned_cols=56  Identities=25%  Similarity=0.301  Sum_probs=51.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEE-EEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVG-DIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~-~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..+|.|. .+.++.++.+++++|||||+|.+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~   61 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD   61 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCC
Confidence            345569999999999999999999999999999 99999999999999999999975

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=6e-17  Score=79.21  Aligned_cols=55  Identities=33%  Similarity=0.672  Sum_probs=51.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||+.+++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   59 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMF   59 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECC
Confidence            4556899999999999999999999999999999999998899999999999976

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.72  E-value=2.3e-17  Score=81.13  Aligned_cols=55  Identities=27%  Similarity=0.401  Sum_probs=50.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..||.|..+.++.++ +++++|||||+|.+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~   59 (102)
T 2xs2_A            5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYN   59 (102)
T ss_dssp             CEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECC
Confidence            34455899999999999999999999999999999999998 99999999999976

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=5.7e-17  Score=80.20  Aligned_cols=55  Identities=20%  Similarity=0.342  Sum_probs=49.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEE-EEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD-IYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..+|.|.. +.++.+ .+++++|||||+|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~   66 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFAS   66 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECC
Confidence            4455689999999999999999999999999987 778887 799999999999976

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.72  E-value=8.5e-17  Score=79.26  Aligned_cols=57  Identities=23%  Similarity=0.364  Sum_probs=51.5

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +......++|||+|||+++++++|+++|..+| |..+.++.++.+++++|||||+|.+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~   65 (103)
T 2dng_A            9 ELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDE   65 (103)
T ss_dssp             CCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESS
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECC
Confidence            33455568999999999999999999999996 9999999999899999999999976

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.72  E-value=5.3e-17  Score=78.84  Aligned_cols=57  Identities=26%  Similarity=0.371  Sum_probs=50.6

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +...+..++|||+|||+.+++++|+++|..+|.|..+.++.++. ++++|||||+|.+
T Consensus        10 ~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~   66 (95)
T 2ywk_A           10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKH   66 (95)
T ss_dssp             --CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESS
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECC
Confidence            44556668999999999999999999999999999999999874 9999999999986

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.72  E-value=5.7e-17  Score=77.58  Aligned_cols=54  Identities=22%  Similarity=0.383  Sum_probs=49.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||.++++++|+++|+.+|.|..+.++.++.+++++|||||+|.+
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   57 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN   57 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECC
Confidence            345899999999999999999999999999999999998899999999999975

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=9e-17  Score=78.02  Aligned_cols=54  Identities=31%  Similarity=0.538  Sum_probs=50.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||.++++++|+++|..+|.|..+.++.++.+++++|||||+|.+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~   56 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSD   56 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECC
Confidence            345899999999999999999999999999999999998899999999999976

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.72  E-value=3.8e-17  Score=86.06  Aligned_cols=53  Identities=23%  Similarity=0.357  Sum_probs=49.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccC--CEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+++++++|+++|..||  .|..+.++.++.+|+++|||||+|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~  108 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVAS  108 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECC
Confidence            347999999999999999999999999  99999999999999999999999976

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=6e-17  Score=79.92  Aligned_cols=57  Identities=16%  Similarity=0.324  Sum_probs=51.1

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCC-CCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFT-RESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~-~~~~g~~fv~f~~   64 (65)
                      +......++|||+|||+.+++++|+++|..+| |..+.++.++.+ ++++|||||+|.+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~   66 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED   66 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESS
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECC
Confidence            33445568999999999999999999999999 999999999877 9999999999975

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.72  E-value=4e-17  Score=81.78  Aligned_cols=56  Identities=23%  Similarity=0.165  Sum_probs=51.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~   76 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN   76 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSS
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECC
Confidence            33455899999999999999999999999999999999998899999999999975

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=5.1e-17  Score=79.85  Aligned_cols=58  Identities=29%  Similarity=0.499  Sum_probs=52.9

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .......++|||+|||+++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus         6 ~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   63 (102)
T 1x5s_A            6 SGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN   63 (102)
T ss_dssp             CCCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSS
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECC
Confidence            3345566999999999999999999999999999999999998899999999999976

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.71  E-value=1.3e-16  Score=78.74  Aligned_cols=55  Identities=25%  Similarity=0.343  Sum_probs=50.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||..+++++|+++|..||.|..+.++.++ +++++|||||+|.+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~   65 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSS   65 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCC
Confidence            33456899999999999999999999999999999999987 89999999999975

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.71  E-value=5.8e-17  Score=77.26  Aligned_cols=54  Identities=35%  Similarity=0.442  Sum_probs=50.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||.++++++|+++|..+|.|..+.++.++.+++++|||||+|.+
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   58 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL   58 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECC
Confidence            455899999999999999999999999999999999998899999999999976

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.1e-17  Score=83.91  Aligned_cols=52  Identities=33%  Similarity=0.586  Sum_probs=49.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||+++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~   78 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS   78 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCC
Confidence            4899999999999999999999999999999999998899999999999975

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.71  E-value=4.8e-17  Score=88.56  Aligned_cols=54  Identities=33%  Similarity=0.384  Sum_probs=49.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++.+++++|||||+|.+
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~   66 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ   66 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCC
Confidence            345799999999999999999999999999999999999999999999999975

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.71  E-value=7.1e-17  Score=82.64  Aligned_cols=55  Identities=20%  Similarity=0.279  Sum_probs=48.7

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEE--EEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVG--DIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~--~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .......+|||+|||+++++++|+++|..| .|.  .+.++.++. |+++|||||+|.+
T Consensus        37 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~   93 (126)
T 2hgm_A           37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFAS   93 (126)
T ss_dssp             TCSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECC
Confidence            344556899999999999999999999999 677  889999876 9999999999986

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.71  E-value=7.1e-17  Score=82.68  Aligned_cols=57  Identities=39%  Similarity=0.513  Sum_probs=52.4

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+..++|||+|||+++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~   97 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN   97 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECC
Confidence            344556899999999999999999999999999999999999899999999999976

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=1e-16  Score=79.00  Aligned_cols=55  Identities=24%  Similarity=0.205  Sum_probs=51.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhc-cCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFER-CGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~-~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +....++|||+|||+++++++|+++|.. ||.|..+.++.++ +++++|||||+|.+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~   60 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTD   60 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECC
Confidence            4456689999999999999999999999 9999999999998 99999999999976

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.71  E-value=1e-16  Score=76.11  Aligned_cols=51  Identities=25%  Similarity=0.298  Sum_probs=48.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+|||+|||.++++++|+++|..+|.|..+.++.++.+++++|||||+|.+
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~   52 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS   52 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECC
Confidence            689999999999999999999999999999999998899999999999976

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.70  E-value=1.3e-16  Score=76.58  Aligned_cols=52  Identities=31%  Similarity=0.606  Sum_probs=49.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||.++++++|+++|..+|.|..+.++.++.+++++|||||+|.+
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   57 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD   57 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECC
Confidence            4799999999999999999999999999999999998899999999999986

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.70  E-value=1.3e-17  Score=82.05  Aligned_cols=53  Identities=23%  Similarity=0.335  Sum_probs=50.0

Q ss_pred             CCcEEEEecCCC------CCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTY------RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~------~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+      .+++++|+++|+.||.|..+.++.++.+++++|||||+|.+
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~   63 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGS   63 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESS
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECC
Confidence            358999999999      99999999999999999999999999999999999999976

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=1.9e-16  Score=77.57  Aligned_cols=55  Identities=20%  Similarity=0.354  Sum_probs=50.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||..+++++|+++|..||.|..+.++.++ +++++|||||+|.+
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~   67 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYEN   67 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECC
Confidence            34456899999999999999999999999999999999987 99999999999976

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.70  E-value=1.6e-17  Score=80.30  Aligned_cols=51  Identities=31%  Similarity=0.481  Sum_probs=46.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccC--CEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+|||+|||+++++++|+++|+.+|  .|..+.++.++.+|+++|||||+|.+
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~   54 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGS   54 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-C
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECC
Confidence            5799999999999999999999999  99999999999999999999999975

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.70  E-value=1.1e-16  Score=81.23  Aligned_cols=58  Identities=26%  Similarity=0.330  Sum_probs=52.7

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +......++|||+|||+.+++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        16 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   73 (126)
T 3ex7_B           16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET   73 (126)
T ss_dssp             BCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECC
Confidence            3445556899999999999999999999999999999999998899999999999976

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.70  E-value=1.3e-16  Score=78.98  Aligned_cols=58  Identities=17%  Similarity=0.350  Sum_probs=49.6

Q ss_pred             CCCCCCCCCcEEEEecCCCCC------CHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           5 RPPPRIEGMVSLKVDNLTYRT------TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         5 ~~~~~~~~~~~l~v~~l~~~~------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++......++|||+|||+.+      ++++|+++|+.||.|..+.++  +.+|+++|||||+|.+
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~   70 (105)
T 2nlw_A            7 RPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYAS   70 (105)
T ss_dssp             CCCSCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECS
T ss_pred             CCCCCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECC
Confidence            344444556899999999999      679999999999999999887  4689999999999986

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=4.6e-17  Score=81.47  Aligned_cols=52  Identities=33%  Similarity=0.487  Sum_probs=49.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||+++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~   76 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE   76 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCc
Confidence            3799999999999999999999999999999999999899999999999976

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=3.7e-17  Score=81.85  Aligned_cols=59  Identities=20%  Similarity=0.423  Sum_probs=50.7

Q ss_pred             CCCCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           4 GRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         4 ~~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.+++......+|||+|||+++++++|+++|..+ .|..+.++.++. |+++|||||+|.+
T Consensus         7 ~~~~~~~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~   65 (109)
T 2dnn_A            7 GKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLS   65 (109)
T ss_dssp             CCCCCCCHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSS
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECC
Confidence            3344444556899999999999999999999999 889999999874 9999999999975

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=3.7e-17  Score=80.34  Aligned_cols=58  Identities=33%  Similarity=0.390  Sum_probs=52.7

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .......++|||+|||+.+++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus         6 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   63 (102)
T 2cqb_A            6 SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL   63 (102)
T ss_dssp             SCSCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSS
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECC
Confidence            3345566899999999999999999999999999999999998899999999999975

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.70  E-value=2.1e-16  Score=81.08  Aligned_cols=56  Identities=34%  Similarity=0.420  Sum_probs=51.6

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||..+++++|+++|..+|.|..+.++.++.+++++|||||+|.+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~  114 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL  114 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESC
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECC
Confidence            34456899999999999999999999999999999999998899999999999976

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.70  E-value=1.3e-16  Score=82.03  Aligned_cols=56  Identities=32%  Similarity=0.510  Sum_probs=51.6

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +....++|||+|||.++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   93 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS   93 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECC
Confidence            34455899999999999999999999999999999999998899999999999975

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=6.7e-17  Score=79.93  Aligned_cols=55  Identities=18%  Similarity=0.185  Sum_probs=49.2

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......++|||+|||+++++++|+++|..+|.+ .+.++.++ +++++|||||+|.+
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~   64 (102)
T 1wez_A           10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFAT   64 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECC
Confidence            344556899999999999999999999999954 89999997 99999999999986

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.70  E-value=1.5e-16  Score=77.52  Aligned_cols=52  Identities=19%  Similarity=0.316  Sum_probs=49.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||..+++++|+++|+.+|.|..+.++.++.+++++|||||+|.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~   53 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD   53 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESS
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECC
Confidence            4799999999999999999999999999999999998899999999999975

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.70  E-value=2.1e-16  Score=78.22  Aligned_cols=57  Identities=25%  Similarity=0.300  Sum_probs=51.5

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +......++|||+|||+.+++++|+++|..||.|..+.++.++ +++++|||||+|.+
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~   79 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFER   79 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECC
Confidence            3445667899999999999999999999999999999999998 99999999999975

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.69  E-value=1.9e-16  Score=83.62  Aligned_cols=57  Identities=26%  Similarity=0.302  Sum_probs=51.5

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......++|||+|||+.+++++|+.+|..||.|..+.++.++.+|+++|||||+|.+
T Consensus        67 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~  123 (165)
T 1rk8_A           67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET  123 (165)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECC
Confidence            344556789999999999999999999999999999999998899999999999976

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.6e-16  Score=79.27  Aligned_cols=57  Identities=30%  Similarity=0.279  Sum_probs=51.7

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEE--------EEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVG--------DIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+....++|||+|||+.+++++|+++|..+|.|.        .+.++.++.+++++|||||+|.+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~   74 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED   74 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSS
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECC
Confidence            3455668999999999999999999999999998        68999998899999999999976

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=3.5e-17  Score=76.81  Aligned_cols=51  Identities=35%  Similarity=0.652  Sum_probs=48.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++|||+|||.++++++|+++|+.+|.|..+.++.++.+++++|||||+|.+
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~   51 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD   51 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcC
Confidence            479999999999999999999999999999999998899999999999976

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1e-16  Score=80.43  Aligned_cols=55  Identities=16%  Similarity=0.170  Sum_probs=49.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCE-EEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEV-GDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i-~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..+|.| ..+.++.++ +++++|||||+|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~   66 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKN   66 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSS
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECC
Confidence            34456899999999999999999999999999 788999998 99999999999975

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.68  E-value=6.4e-17  Score=75.68  Aligned_cols=50  Identities=34%  Similarity=0.538  Sum_probs=47.6

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +|||+|||+++++++|+++|+.+|.|..+.++.++.+++++|||||+|.+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   50 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES   50 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECC
Confidence            58999999999999999999999999999999998899999999999976

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=2.8e-16  Score=75.88  Aligned_cols=57  Identities=14%  Similarity=0.178  Sum_probs=51.0

Q ss_pred             CCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         6 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.......++|||+|||+++++++|+++|..+ .|..+.++.+ .+|+++|||||+|.+
T Consensus         3 ~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~   59 (91)
T 2dgw_A            3 SGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSN   59 (91)
T ss_dssp             CCCCCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSS
T ss_pred             CCCCCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECC
Confidence            34455667999999999999999999999999 8999999998 799999999999975

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=5.7e-16  Score=77.33  Aligned_cols=56  Identities=27%  Similarity=0.259  Sum_probs=50.8

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+..++|||+|||.++++++|+++|..||.|..+.++.++ +++++|||||+|.+
T Consensus        10 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~   65 (114)
T 2do0_A           10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQ   65 (114)
T ss_dssp             CCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECC
Confidence            344556899999999999999999999999999999999987 69999999999976

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.68  E-value=2e-16  Score=79.68  Aligned_cols=55  Identities=29%  Similarity=0.486  Sum_probs=50.6

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.+..++|||+|||.++++++|+++|+.||.|..+.++.+. +++++|||||+|.+
T Consensus         3 e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~   57 (116)
T 2fy1_A            3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFEN   57 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECC
Confidence            34556899999999999999999999999999999999987 99999999999975

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.1e-16  Score=77.81  Aligned_cols=53  Identities=26%  Similarity=0.336  Sum_probs=49.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEE-EEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||..+++++|+++|..+|.|..+ .++.++.++.++|||||+|.+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~   57 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFAS   57 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECC
Confidence            45899999999999999999999999999999 999998899999999999976

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.68  E-value=4.3e-16  Score=81.50  Aligned_cols=54  Identities=26%  Similarity=0.536  Sum_probs=50.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||..+++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   90 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYS   90 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECC
Confidence            456899999999999999999999999999999999999999999999999976

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.68  E-value=5.5e-17  Score=79.73  Aligned_cols=55  Identities=16%  Similarity=0.350  Sum_probs=47.6

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecC-CCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-FTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~-~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..+| |..+.++.++ .+|+++|||||+|.+
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~   70 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED   70 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECC
Confidence            445568999999999999999999999999 9999999887 689999999999976

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=4.5e-16  Score=76.58  Aligned_cols=54  Identities=26%  Similarity=0.363  Sum_probs=49.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+.+++++|+++|..||.|..+.++.+  +++++|||||+|.+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~   64 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSS   64 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECC
Confidence            3455689999999999999999999999999999999887  89999999999975

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.67  E-value=2.6e-16  Score=86.96  Aligned_cols=53  Identities=30%  Similarity=0.446  Sum_probs=49.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccC--CEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCG--EVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+||++++++++|+++|..||  .|..+.++.++.+++++|||||+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~  121 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGS  121 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECC
Confidence            457899999999999999999999999  99999999999999999999999986

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.67  E-value=4.5e-17  Score=76.14  Aligned_cols=50  Identities=32%  Similarity=0.512  Sum_probs=47.7

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +|||+|||+++++++|+++|+.+|.|..+.++.++.++.++|||||+|.+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   50 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKE   50 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSS
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECC
Confidence            58999999999999999999999999999999998899999999999986

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=4.7e-16  Score=77.70  Aligned_cols=54  Identities=26%  Similarity=0.381  Sum_probs=50.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||.++++++|+++|..||.|..+.++.++ ++.++|||||+|.+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~   75 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMES   75 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECC
Confidence            3456899999999999999999999999999999999998 99999999999975

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.67  E-value=3.9e-16  Score=81.64  Aligned_cols=54  Identities=78%  Similarity=1.276  Sum_probs=50.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+|||+|||+++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~  121 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD  121 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECC
Confidence            445899999999999999999999999999999999998899999999999976

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=3e-17  Score=80.87  Aligned_cols=54  Identities=26%  Similarity=0.460  Sum_probs=50.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+.+++++|+++|..||.|..+.++.++.++.++|||||+|.+
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~   59 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD   59 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSC
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECC
Confidence            345899999999999999999999999999999999998899999999999976

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.67  E-value=2.7e-16  Score=79.02  Aligned_cols=51  Identities=22%  Similarity=0.335  Sum_probs=45.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+|||+|||+++++++|+++|..||.|..+.++.+.  +.++|||||+|.+
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~   54 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFET   54 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECC
Confidence            34789999999999999999999999999999999875  4479999999976

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=4.5e-16  Score=77.18  Aligned_cols=54  Identities=20%  Similarity=0.282  Sum_probs=49.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCC-EEEEEEe-ecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIP-RDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~-i~~~~~~-~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+++++++|+++|..+|. |..+.++ .++.++.++|||||+|.+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~   61 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES   61 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESS
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecC
Confidence            34589999999999999999999999998 9999888 788889999999999975

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=2e-16  Score=77.17  Aligned_cols=54  Identities=30%  Similarity=0.482  Sum_probs=48.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCC---CCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRF---TRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~---~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+++++++|+++|..||.|..+.++.++.   ++.++|||||+|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~   59 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKK   59 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECC
Confidence            3458999999999999999999999999999999988765   66899999999975

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=3.5e-16  Score=77.92  Aligned_cols=50  Identities=12%  Similarity=0.159  Sum_probs=44.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|++||.|.++.++.+      ||||||+|++
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~   61 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNT   61 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECC
Confidence            3455689999999999999999999999999999988764      6999999975

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=7.4e-17  Score=81.85  Aligned_cols=55  Identities=15%  Similarity=0.140  Sum_probs=48.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||+++++++|+++|..||.|..+.++.+..+++++|||||+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~   76 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN   76 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECC
Confidence            3455899999999999999999999999998775566666799999999999986

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.66  E-value=8.3e-16  Score=74.19  Aligned_cols=54  Identities=26%  Similarity=0.302  Sum_probs=48.7

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..+|.|..+.++.  .+++++|||||+|.+
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~--~~g~~~g~afV~f~~   57 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFES   57 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEE--SSSCEEEEEEEEESS
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEc--cCCCcceEEEEEECC
Confidence            445568999999999999999999999999999998887  488999999999975

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.66  E-value=7e-16  Score=78.12  Aligned_cols=55  Identities=25%  Similarity=0.342  Sum_probs=50.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||..+++++|+++|..||.|..+.++.++ +++++|||||+|.+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~   85 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFER   85 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECC
Confidence            34555899999999999999999999999999999999988 99999999999976

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.66  E-value=3.6e-16  Score=75.60  Aligned_cols=49  Identities=33%  Similarity=0.478  Sum_probs=43.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+|||+|||+++++++|+++|+.||.|.++.++.+     ++|||||+|.+
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~   57 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFAD   57 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECC
Confidence            44589999999999999999999999999999988763     78999999976

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.66  E-value=3.2e-16  Score=79.31  Aligned_cols=52  Identities=31%  Similarity=0.611  Sum_probs=49.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   87 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE   87 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECC
Confidence            4799999999999999999999999999999999998899999999999975

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.66  E-value=6.6e-17  Score=77.90  Aligned_cols=51  Identities=29%  Similarity=0.563  Sum_probs=48.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++|||+|||.++++++|+++|+.+|.|..+.++.++.+++++|||||+|.+
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   52 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE   52 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECT
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECC
Confidence            689999999999999999999999999999999998899999999999986

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.66  E-value=3.1e-16  Score=81.98  Aligned_cols=53  Identities=34%  Similarity=0.540  Sum_probs=50.2

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+++++++|+++|+.+|.|..+.++.++.+|+++|||||+|.+
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~   54 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEK   54 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEcc
Confidence            45899999999999999999999999999999999998899999999999976

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.66  E-value=1.6e-16  Score=82.20  Aligned_cols=55  Identities=18%  Similarity=0.223  Sum_probs=49.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCC---EEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGE---VGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +....++|||+|||+++++++|+++|..+|.   |..+.++.++. |+++|||||+|.+
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~   97 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGS   97 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECC
Confidence            3455689999999999999999999999998   78899999976 9999999999976

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=1.5e-16  Score=79.76  Aligned_cols=54  Identities=20%  Similarity=0.309  Sum_probs=48.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCC---CCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFT---RESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~---~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||+++++++|+++|..||.|. +.++.+..+   |+++|||||+|.+
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~   61 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQE   61 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSS
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECC
Confidence            34568999999999999999999999999998 778877766   7999999999975

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.66  E-value=1.3e-16  Score=79.24  Aligned_cols=56  Identities=18%  Similarity=0.322  Sum_probs=50.2

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCC---EEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGE---VGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+....++|||+|||+++++++|+++|..+|.   |..+.++.++. |+++|||||+|.+
T Consensus         6 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~   64 (107)
T 2lmi_A            6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMES   64 (107)
T ss_dssp             CCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSS
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECC
Confidence            34556689999999999999999999999887   88899999876 9999999999975

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.9e-15  Score=74.36  Aligned_cols=55  Identities=29%  Similarity=0.428  Sum_probs=48.4

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......++|||+|||+.+++++|+++|..||.|..+.++.++.  .++|||||+|.+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~   64 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFEN   64 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECC
Confidence            3455568999999999999999999999999999999988753  389999999975

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.66  E-value=2.2e-16  Score=79.69  Aligned_cols=55  Identities=20%  Similarity=0.240  Sum_probs=49.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCC---EEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGE---VGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..+|.   |..+.++.++. |+++|||||+|.+
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~   70 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELES   70 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSS
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECC
Confidence            3455689999999999999999999999998   88999999875 9999999999975

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=1.4e-16  Score=77.75  Aligned_cols=56  Identities=16%  Similarity=0.138  Sum_probs=50.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+..++|||+|||+++++++|+++|..+|.|..+.++.++.+++++|||||+|.+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~   66 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES   66 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECC
Confidence            34455899999999999999999999999999877778888899999999999975

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.8e-15  Score=74.44  Aligned_cols=55  Identities=16%  Similarity=0.178  Sum_probs=48.3

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......++|||+|||+.+++++|+++|..||.|..+.++.++.+  ++|||||+|.+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~   64 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYE   64 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESS
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECC
Confidence            34556689999999999999999999999999999999887533  68999999975

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.65  E-value=3.9e-16  Score=80.18  Aligned_cols=51  Identities=12%  Similarity=0.115  Sum_probs=48.9

Q ss_pred             cEEEEecC----CCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNL----TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l----~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+|||+||    |+.+++.+|+.+|+.||+|..+.++.|+.||.++|||||+|.+
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d   57 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYAS   57 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC-
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECC
Confidence            68999999    9999999999999999999999999999999999999999973

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.65  E-value=5e-16  Score=73.68  Aligned_cols=49  Identities=16%  Similarity=0.421  Sum_probs=44.6

Q ss_pred             cEEEEecCCCCC------CHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRT------TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++|||+|||..+      ++++|+++|+.||.|..+.++  +.+|+++|||||+|.+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~   56 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYAS   56 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESS
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECC
Confidence            689999999999      679999999999999999876  4689999999999975

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.64  E-value=5.7e-16  Score=74.14  Aligned_cols=53  Identities=25%  Similarity=0.466  Sum_probs=48.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCC-cccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRE-SRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~-~~g~~fv~f~~   64 (65)
                      ..++|||+|||.++++++|+++|..+|.|..+.++.++.++. ++|||||+|.+
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~   56 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFEN   56 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEec
Confidence            458999999999999999999999999999999998877666 89999999976

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1e-15  Score=77.70  Aligned_cols=50  Identities=12%  Similarity=0.157  Sum_probs=44.6

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+..++|||+|||+++++++|+++|++||.|.++.++.+      +|||||+|++
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~   76 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNT   76 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECC
Confidence            4445689999999999999999999999999999988764      7999999976

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.63  E-value=2.1e-16  Score=76.69  Aligned_cols=54  Identities=17%  Similarity=0.167  Sum_probs=48.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+++++++|+++|..+|.|..+.++.++.+++++|||||+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~   66 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES   66 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECC
Confidence            345899999999999999999999999999888888888899999999999975

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.62  E-value=2.7e-16  Score=81.59  Aligned_cols=54  Identities=17%  Similarity=0.133  Sum_probs=46.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..+| +..+.++.++. ++++|||||+|.+
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~   95 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFAT   95 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCC
Confidence            344568999999999999999999999999 66999999875 9999999999975

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.62  E-value=2e-15  Score=79.24  Aligned_cols=53  Identities=30%  Similarity=0.497  Sum_probs=49.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCC--CcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTR--ESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~--~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+++++++|+++|..+|.|..+.++.++.++  +++|||||+|.+
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~   56 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYT   56 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESS
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECC
Confidence            45899999999999999999999999999999999998776  899999999975

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=4.1e-15  Score=73.54  Aligned_cols=49  Identities=18%  Similarity=0.184  Sum_probs=43.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+..++|||+|||+.+++++|+++|.+||.|..+.++.+      +|||||+|++
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~   60 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELAT   60 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECC
Confidence            344589999999999999999999999999999977653      7999999975

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=3.5e-15  Score=72.77  Aligned_cols=52  Identities=21%  Similarity=0.293  Sum_probs=46.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHH----HHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLR----RVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||+++++++|+    ++|..||.|..+.++.++.+   +|||||+|.+
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~   61 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMEN   61 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECC
Confidence            3455899999999999999999    99999999999999988755   8999999975

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=6.3e-16  Score=78.79  Aligned_cols=53  Identities=19%  Similarity=0.267  Sum_probs=47.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCE----EEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEV----GDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i----~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+|||+|||+++++++|+++|..||.|    ..+.++.+ .+|+++|||||+|.+
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~   77 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFAC   77 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECC
Confidence            455899999999999999999999999875    57888888 489999999999975

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.62  E-value=5.4e-15  Score=73.09  Aligned_cols=50  Identities=12%  Similarity=0.162  Sum_probs=43.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+++|||+|||+.+++++|+++|++||.|.++.++.      .||+|||+|++
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~   66 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFED   66 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESS
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECC
Confidence            344568999999999999999999999999999998764      46999999975

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=2.5e-15  Score=74.85  Aligned_cols=55  Identities=31%  Similarity=0.479  Sum_probs=48.4

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......++|||+|||.++++++|+++|+.||.|..+.++.++  +.++|||||+|.+
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~   78 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFEN   78 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCC
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECC
Confidence            344556899999999999999999999999999999998874  3489999999986

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.61  E-value=6.2e-15  Score=73.18  Aligned_cols=50  Identities=16%  Similarity=0.167  Sum_probs=43.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+.+++++|+++|.+||.|..+.++.+      ||||||+|++
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~   60 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFEN   60 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECC
Confidence            3455689999999999999999999999999999887652      7999999975

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.61  E-value=4.3e-15  Score=77.33  Aligned_cols=52  Identities=29%  Similarity=0.497  Sum_probs=49.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||.++++++|+++|+.+|.|..+.++.++.+|+++|||||+|.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~   53 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYID   53 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECC
Confidence            4799999999999999999999999999999999998899999999999975

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=1e-14  Score=72.37  Aligned_cols=53  Identities=26%  Similarity=0.335  Sum_probs=46.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||.++++++|+++|..||.|..+.+..   ++.++|||||+|.+
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~   70 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFED   70 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECC
Confidence            445568999999999999999999999999999988754   45689999999976

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.60  E-value=3.8e-15  Score=77.80  Aligned_cols=53  Identities=30%  Similarity=0.345  Sum_probs=49.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||.++++++|+++|+.+|.|..+.++.++.++.++|||||+|.+
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   54 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTS   54 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESS
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECC
Confidence            34899999999999999999999999999999999998899999999999975

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=1.3e-14  Score=72.06  Aligned_cols=51  Identities=24%  Similarity=0.306  Sum_probs=45.1

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++.....++|||+|||+++++++|+++|..||.|..+.++.+       |||||+|.+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~   59 (108)
T 1x4c_A            9 PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVR   59 (108)
T ss_dssp             CCCCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECC
Confidence            334556789999999999999999999999999999988765       899999975

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.59  E-value=5.5e-15  Score=79.08  Aligned_cols=53  Identities=26%  Similarity=0.342  Sum_probs=49.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+.+++++|+++|..||.|..+.++.++ ++.++|||||+|.+
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~  138 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFER  138 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCC
Confidence            445899999999999999999999999999999999987 99999999999975

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.59  E-value=2e-14  Score=74.72  Aligned_cols=57  Identities=23%  Similarity=0.270  Sum_probs=52.2

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......++|||+|||..+++++|+++|+.+|.|..+.++.++.++.++|+|||+|.+
T Consensus        82 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~  138 (166)
T 3md3_A           82 SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS  138 (166)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESC
T ss_pred             CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCC
Confidence            344556899999999999999999999999999999999998899999999999976

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.59  E-value=9.5e-15  Score=74.75  Aligned_cols=54  Identities=17%  Similarity=0.332  Sum_probs=45.1

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHH----HHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLR----RVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......++|||+|||+.+++++|+    ++|+.||.|.++.+.   .+++++|||||+|.+
T Consensus        24 ~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~---~~~~~rG~aFV~F~~   81 (127)
T 2a3j_A           24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFAT   81 (127)
T ss_dssp             CCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEESS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEECC
Confidence            344556899999999999998865    689999999888664   378899999999975

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=5e-15  Score=73.88  Aligned_cols=56  Identities=16%  Similarity=0.201  Sum_probs=48.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHH---HHhhccCCEEEEEEeecCCCC---CcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLR---RVFERCGEVGDIYIPRDRFTR---ESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~---~~f~~~g~i~~~~~~~~~~~~---~~~g~~fv~f~~   64 (65)
                      +.....+|||+|||+++++++|+   ++|..||.|..+.++.++.++   .++|||||+|.+
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~   72 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR   72 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESS
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECc
Confidence            44556899999999999999999   999999999999998887643   566999999975

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=2.2e-15  Score=72.32  Aligned_cols=48  Identities=38%  Similarity=0.586  Sum_probs=43.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+++++++|+++|..||.|..+.++.+     ++|||||+|.+
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~   51 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFAD   51 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECC
Confidence            4589999999999999999999999999999987653     78999999975

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.59  E-value=1.3e-14  Score=76.13  Aligned_cols=55  Identities=20%  Similarity=0.353  Sum_probs=51.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||..+++++|+++|..+|.|..+.++.++.++.++|||||+|.+
T Consensus        91 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~  145 (172)
T 2g4b_A           91 LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD  145 (172)
T ss_dssp             CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESS
T ss_pred             CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCC
Confidence            3446899999999999999999999999999999999998899999999999986

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=2e-14  Score=68.38  Aligned_cols=53  Identities=25%  Similarity=0.340  Sum_probs=46.3

Q ss_pred             CCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         6 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+......++|||+|||..+++++|+++|..||.|..+.++.      ++|||||+|.+
T Consensus         5 ~~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~------~kg~afV~f~~   57 (85)
T 2ytc_A            5 SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFAT   57 (85)
T ss_dssp             CCCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESS
T ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC------CCCEEEEEECC
Confidence            344556678999999999999999999999999999998876      37999999976

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.58  E-value=1e-14  Score=77.78  Aligned_cols=53  Identities=32%  Similarity=0.407  Sum_probs=50.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||.++++++|+++|..||.|..+.++.++.++.++|||||+|.+
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~  155 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD  155 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECC
Confidence            44899999999999999999999999999999999998899999999999976

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.58  E-value=9.2e-15  Score=86.85  Aligned_cols=54  Identities=30%  Similarity=0.487  Sum_probs=50.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+|||+|||+.+++++|..+|..||.|..+.++.++.+++++|||||+|.+
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~  153 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEH  153 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeecc
Confidence            344799999999999999999999999999999999998899999999999986

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.58  E-value=3.5e-16  Score=76.74  Aligned_cols=53  Identities=19%  Similarity=0.164  Sum_probs=46.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+++++++|+++|..+|.|.. .++.++.+++++|||||+|.+
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~   67 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFES   67 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECC
Confidence            35689999999999999999999999998776 566666789999999999975

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.58  E-value=8.9e-15  Score=72.48  Aligned_cols=50  Identities=16%  Similarity=0.233  Sum_probs=44.0

Q ss_pred             CCCCCcEEEEecCCC-CCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+..++|||+|||+ .+++++|+++|.+||.|..+.++.+      +|||||+|++
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~   61 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMAT   61 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECC
Confidence            344568999999999 9999999999999999999988764      4899999975

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.58  E-value=1.1e-14  Score=78.59  Aligned_cols=52  Identities=29%  Similarity=0.504  Sum_probs=47.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||.++++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~   79 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV   79 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCC
Confidence            4799999999999999999999999999999999998899999999999975

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=8.3e-16  Score=76.83  Aligned_cols=56  Identities=30%  Similarity=0.242  Sum_probs=44.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||..+++++|+++|..||.|..+.+..+..+++++|||||+|.+
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~   76 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPN   76 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECC
Confidence            33456899999999999999999999999988433222222388899999999976

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=1.4e-14  Score=71.03  Aligned_cols=53  Identities=26%  Similarity=0.505  Sum_probs=45.5

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......++|||+|||+++++++|+++|..+|.|   .++.+ .+++++|||||+|.+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~   62 (101)
T 2fc9_A           10 TWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFAS   62 (101)
T ss_dssp             CCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSS
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECC
Confidence            344566999999999999999999999999977   45555 689999999999975

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.35  E-value=1.8e-16  Score=79.58  Aligned_cols=55  Identities=22%  Similarity=0.170  Sum_probs=50.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEE--------EEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGD--------IYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~--------~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||..+++++|+++|..||.|..        +.++.++.+++++|||||+|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~   66 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD   66 (116)
Confidence            345689999999999999999999999999988        8888888899999999999986

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.56  E-value=3.1e-14  Score=71.14  Aligned_cols=51  Identities=27%  Similarity=0.430  Sum_probs=45.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +..++|||+|||+.+++++|+++|..||.|..+.++.+   +.++|||||+|.+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~   56 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYED   56 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECC
Confidence            44589999999999999999999999999999988764   4568999999975

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.6e-14  Score=70.85  Aligned_cols=55  Identities=31%  Similarity=0.361  Sum_probs=47.0

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .......++|||+|||+++++++|+++|..++   .+.++.++.+++++|||||+|.+
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~   63 (102)
T 2fc8_A            9 NARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNS   63 (102)
T ss_dssp             SSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSS
T ss_pred             CCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECC
Confidence            34556668999999999999999999999774   56677788899999999999975

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.55  E-value=3.7e-14  Score=73.98  Aligned_cols=56  Identities=34%  Similarity=0.427  Sum_probs=51.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||..+++++|+++|+.+|.|..+.++.++.++.++|+|||+|.+
T Consensus        85 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~  140 (168)
T 1b7f_A           85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK  140 (168)
T ss_dssp             STTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             ccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECC
Confidence            44556899999999999999999999999999999999998899999999999976

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.55  E-value=2.7e-14  Score=74.31  Aligned_cols=56  Identities=27%  Similarity=0.318  Sum_probs=51.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......+|||+|||..+++++|+++|+.+|.|..+.++.++.+|.++|||||+|.+
T Consensus        84 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~  139 (167)
T 1fxl_A           84 ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDK  139 (167)
T ss_dssp             GGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             ccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCC
Confidence            33455899999999999999999999999999999999998899999999999976

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.55  E-value=5.9e-14  Score=74.92  Aligned_cols=54  Identities=19%  Similarity=0.324  Sum_probs=50.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||..+++++|+++|..+|.|..+.++.++.++.++|||||+|.+
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~  165 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD  165 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECC
Confidence            455899999999999999999999999999999999998899999999999986

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.55  E-value=3e-14  Score=77.04  Aligned_cols=51  Identities=24%  Similarity=0.283  Sum_probs=47.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||+.+++++|+++|+.||.|..++++.+. ++.++|||||+|.+
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~  159 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDS  159 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESS
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECC
Confidence            4799999999999999999999999999999999886 68999999999986

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.54  E-value=1.8e-14  Score=72.48  Aligned_cols=49  Identities=16%  Similarity=0.216  Sum_probs=43.2

Q ss_pred             CCCCcEEEEecCCCC-CCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||++ +++++|+++|.+||.|.++.++.      .+|||||+|++
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~   71 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMET   71 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSS
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECC
Confidence            344689999999998 99999999999999999998863      47999999975

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.54  E-value=2.5e-14  Score=69.27  Aligned_cols=47  Identities=21%  Similarity=0.215  Sum_probs=42.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+..|||+||++.+++++|+++|.++|.|..+++..      ++|||||+|.+
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~   52 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTT   52 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESS
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECC
Confidence            357899999999999999999999999999998855      68999999976

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=7.5e-14  Score=67.17  Aligned_cols=47  Identities=32%  Similarity=0.517  Sum_probs=42.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||.++++++|+++|..||.|..+.++        +|||||+|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~   51 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIED   51 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECC
Confidence            4456899999999999999999999999999999876        6899999975

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.53  E-value=6.7e-15  Score=71.56  Aligned_cols=53  Identities=28%  Similarity=0.479  Sum_probs=45.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHH----HHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLR----RVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +....++|||+|||.++++++|+    ++|..||.|..+.+..   +++++|||||+|.+
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~   60 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKE   60 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCC
Confidence            34556899999999999999999    9999999999987763   67788999999975

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.53  E-value=2.6e-14  Score=74.32  Aligned_cols=50  Identities=30%  Similarity=0.389  Sum_probs=45.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++|||+|||.++++++|+++|+.+|.|..+.++.++ +++++|||||+|.+
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~   50 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQ   50 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESS
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCC
Confidence            589999999999999999999999999999998886 57899999999975

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.53  E-value=5.9e-14  Score=75.75  Aligned_cols=53  Identities=23%  Similarity=0.446  Sum_probs=50.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||..+++++|+++|..||.|..+.++.++.+++++|||||+|.+
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~  176 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEK  176 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecC
Confidence            44799999999999999999999999999999999998899999999999976

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.53  E-value=5.4e-14  Score=68.68  Aligned_cols=50  Identities=32%  Similarity=0.668  Sum_probs=44.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||..+++++|+++|..||.|..+.+..      .+|||||+|.+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~------~kg~afV~f~~   60 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLET   60 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET------TTTEEEEECSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCEEEEEECC
Confidence            445568999999999999999999999999999998764      37999999986

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.53  E-value=4.7e-14  Score=73.32  Aligned_cols=51  Identities=25%  Similarity=0.398  Sum_probs=45.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+.+++++|+++|..||.|..+.++.+     ++|||||+|.+
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~  119 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFED  119 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECC
Confidence            3455689999999999999999999999999999988775     58999999975

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.52  E-value=8.6e-14  Score=67.76  Aligned_cols=50  Identities=24%  Similarity=0.328  Sum_probs=43.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||.++++++|+++|..||.|..+.+..+      +|||||+|.+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~   62 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYES   62 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECC
Confidence            3445589999999999999999999999999999987643      7899999975

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.52  E-value=2e-14  Score=75.03  Aligned_cols=52  Identities=25%  Similarity=0.359  Sum_probs=49.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+|||+|||..+++++|+++|+.+|.|..+.++.++.++.++|||||+|.+
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~  138 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS  138 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESS
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECC
Confidence            4689999999999999999999999999999999998899999999999975

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.52  E-value=5.6e-14  Score=68.79  Aligned_cols=48  Identities=19%  Similarity=0.254  Sum_probs=42.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||.++++++|+++|..||.|..+.+.      +++|||||+|.+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~   72 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDT   72 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSS
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECC
Confidence            345899999999999999999999999999998876      367999999975

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=1.7e-13  Score=66.43  Aligned_cols=50  Identities=22%  Similarity=0.240  Sum_probs=43.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||+++++++|+++|..||.|..+  +.++.+++   ||||+|.+
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~   54 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGD   54 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESS
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECC
Confidence            3455899999999999999999999999999886  56666665   99999975

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.52  E-value=3.1e-14  Score=71.41  Aligned_cols=51  Identities=14%  Similarity=0.083  Sum_probs=43.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccC-CEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +....+|||+|||+++++++|+++|..+| .|..+.+..    .+++|||||+|.+
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~   76 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPS   76 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECC
Confidence            34568999999999999999999999999 898887643    3578999999975

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=1.1e-13  Score=66.79  Aligned_cols=52  Identities=27%  Similarity=0.349  Sum_probs=45.1

Q ss_pred             CCCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           5 RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         5 ~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++......++|||+|||+.+++++|+++|..||.|..+.++        ++||||+|.+
T Consensus         2 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~   53 (92)
T 2dgt_A            2 SSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMER   53 (92)
T ss_dssp             CCSCCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESC
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECC
Confidence            345566677999999999999999999999999999998875        3599999976

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.51  E-value=2.8e-14  Score=71.61  Aligned_cols=49  Identities=20%  Similarity=0.215  Sum_probs=41.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......+|||+|||+++++++|+++|..||.|..+.++.+       |||||+|.+
T Consensus        12 ~~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~   60 (115)
T 3beg_B           12 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVR   60 (115)
T ss_dssp             -----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESS
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECC
Confidence            3355689999999999999999999999999999988664       999999976

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=9.9e-14  Score=68.81  Aligned_cols=49  Identities=18%  Similarity=0.352  Sum_probs=44.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||..+++++|+++|..||.|..+.++.+      +|||||+|.+
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~   70 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFST   70 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECC
Confidence            345689999999999999999999999999999988765      7999999975

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.51  E-value=1.3e-13  Score=72.29  Aligned_cols=52  Identities=27%  Similarity=0.383  Sum_probs=48.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||..+++++|+++|+.||.|..+.++.++ +|+++|||||+|.+
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~  145 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTT  145 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESS
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECC
Confidence            45899999999999999999999999999999998885 69999999999976

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=8e-14  Score=67.90  Aligned_cols=51  Identities=22%  Similarity=0.242  Sum_probs=42.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+..++|||+|||+++++++|+++|..||.|. +.++.    +.++|||||+|.+
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~   65 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPD   65 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSS
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECC
Confidence            334468999999999999999999999999985 55544    4678999999975

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.50  E-value=3.5e-14  Score=70.91  Aligned_cols=48  Identities=23%  Similarity=0.390  Sum_probs=42.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+.+++++|+++|..||.|..+.++.      .+|||||+|.+
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~   55 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLE   55 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCC
Confidence            3457999999999999999999999999999987753      57899999975

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.50  E-value=6.7e-14  Score=69.63  Aligned_cols=48  Identities=23%  Similarity=0.326  Sum_probs=42.6

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..||.|..+.++        +|||||+|.+
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~   74 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEE   74 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSS
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECC
Confidence            44556899999999999999999999999999998876        6999999975

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.50  E-value=4.6e-14  Score=69.11  Aligned_cols=46  Identities=30%  Similarity=0.517  Sum_probs=42.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++|||+|||.++++++|+++|+.||.|..+.++.+     ++|||||+|.+
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~   46 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFED   46 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECC
Confidence            47999999999999999999999999999988775     78999999975

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.50  E-value=1.4e-13  Score=67.64  Aligned_cols=50  Identities=20%  Similarity=0.321  Sum_probs=43.3

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +......++|||+|||+++++++|+++|..||.|..+.++        +|||||+|.+
T Consensus         5 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~   54 (103)
T 2dgu_A            5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDE   54 (103)
T ss_dssp             CCCCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCC
Confidence            3344556899999999999999999999999999998875        4699999975

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.50  E-value=2.3e-14  Score=69.57  Aligned_cols=51  Identities=25%  Similarity=0.471  Sum_probs=43.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+.+++++|+++|..+|.|..+     ..+++++|||||+|.+
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~   62 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKS   62 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECC
Confidence            34456899999999999999999999999877554     3578899999999975

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.49  E-value=2.3e-13  Score=66.50  Aligned_cols=48  Identities=25%  Similarity=0.386  Sum_probs=42.1

Q ss_pred             CCCCCcEEEEecCCC-CCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+ ++++++|+++|..||.|..+.+        .+|||||+|.+
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i--------~~g~afV~f~~   66 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDN   66 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE--------CSSEEEEEESS
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE--------eCCEEEEEECC
Confidence            445568999999998 9999999999999999999887        27999999975

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.48  E-value=2.1e-13  Score=72.36  Aligned_cols=52  Identities=23%  Similarity=0.269  Sum_probs=44.3

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......+|||+||++.+++++|+++|++||.|.++.+...    ..+|||||+|.+
T Consensus        42 ~ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d   93 (164)
T 1sjr_A           42 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYAD   93 (164)
T ss_dssp             CCCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESC
T ss_pred             CCCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECC
Confidence            3445578999999999999999999999999999987543    257899999975

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=2.4e-13  Score=65.35  Aligned_cols=48  Identities=27%  Similarity=0.393  Sum_probs=42.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +....++|||+|||+.+++++|+++|..||.|..+.++        ++||||+|.+
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~   52 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEK   52 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECC
Confidence            44556899999999999999999999999999999875        3599999976

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.47  E-value=2.4e-13  Score=67.50  Aligned_cols=45  Identities=22%  Similarity=0.396  Sum_probs=41.1

Q ss_pred             CCcEEEEecCCCC-CCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+. +++++|+++|..||.|..+.+        ++|||||+|.+
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~   71 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSN   71 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSS
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECC
Confidence            3489999999999 999999999999999999877        57999999976

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.46  E-value=2.3e-13  Score=66.21  Aligned_cols=48  Identities=27%  Similarity=0.437  Sum_probs=41.2

Q ss_pred             CCCCCcEEEEecCCC-CCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+..++|||+|||+ .+++++|+++|..||.|..+.+.        +|||||+|.+
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~   54 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDN   54 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESC
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECC
Confidence            344568999999998 99999999999999999998773        6999999976

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.46  E-value=3.7e-13  Score=75.37  Aligned_cols=53  Identities=26%  Similarity=0.459  Sum_probs=46.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHH----HHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLR----RVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +....++|||+|||+++++++|+    ++|..||.|..+.+..   +++++|||||+|.+
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~   61 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKE   61 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECC
Confidence            44556899999999999999966    8999999999987765   78899999999976

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.46  E-value=1.1e-14  Score=75.16  Aligned_cols=55  Identities=25%  Similarity=0.228  Sum_probs=43.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEE--E---eecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIY--I---PRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~--~---~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||+.+++++|+++|..||.|..+.  +   +....+++++|||||+|.+
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~  101 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPN  101 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCC
Confidence            44558999999999999999999999999876531  1   1112478999999999975

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.45  E-value=6e-13  Score=74.56  Aligned_cols=53  Identities=19%  Similarity=0.290  Sum_probs=49.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+.+++++|+++|..+|.|..+.++.++.+|.++|||||+|.+
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~  146 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMK  146 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECC
Confidence            34799999999999999999999999999999999998899999999999975

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.45  E-value=4e-13  Score=64.00  Aligned_cols=48  Identities=25%  Similarity=0.400  Sum_probs=42.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcc----C-------CEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERC----G-------EVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+++++++|+++|..+    |       .|..+.+..+      +|||||+|.+
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~   62 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRS   62 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCC
Confidence            345899999999999999999999999    8       8988877643      7999999975

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.45  E-value=3.2e-13  Score=74.12  Aligned_cols=51  Identities=29%  Similarity=0.328  Sum_probs=45.4

Q ss_pred             CCCCCcEEEEecCCC-CCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+ .+++++|+++|+.||.|..+.++.++     +|||||+|.+
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~   81 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMAD   81 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECC
Confidence            445568999999999 99999999999999999999988764     7899999976

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.44  E-value=2.1e-13  Score=68.72  Aligned_cols=48  Identities=27%  Similarity=0.472  Sum_probs=41.4

Q ss_pred             CCCcEEEE--ecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKV--DNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v--~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +..++|||  +||++.+++++|++.|++||.|..+.++.      .+|||||+|.+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~   72 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRT   72 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESS
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECC
Confidence            34578999  77999999999999999999998887643      37999999975

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=4e-13  Score=65.14  Aligned_cols=52  Identities=15%  Similarity=0.115  Sum_probs=44.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEE-EEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..||.|..+ .++.++.++.    |||+|.+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~   63 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSS   63 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESS
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECC
Confidence            33456899999999999999999999999999999 4777765543    9999975

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=2.1e-12  Score=62.95  Aligned_cols=47  Identities=26%  Similarity=0.376  Sum_probs=40.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcc--CCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERC--GEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~--g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||+.+++++|+++|..|  |.|..+.+.        +|||||+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~   60 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSN   60 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESS
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCC
Confidence            3445899999999999999999999999  889887653        6899999976

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.43  E-value=7.2e-13  Score=73.93  Aligned_cols=51  Identities=24%  Similarity=0.290  Sum_probs=48.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+|||+|||..+++++|+++|..||.|..+.++.+ .+|+++|||||+|.+
T Consensus        96 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~  146 (261)
T 3sde_A           96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAA  146 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESS
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCC
Confidence            479999999999999999999999999999999988 599999999999975

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.40  E-value=1.1e-12  Score=71.38  Aligned_cols=50  Identities=20%  Similarity=0.317  Sum_probs=45.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+|||+|||+.+++++|+++|..||.|..+.++.+.  +.++|||||+|.+
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~  152 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFET  152 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESS
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCC
Confidence            4689999999999999999999999999999998874  4479999999976

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=2.3e-13  Score=65.70  Aligned_cols=48  Identities=31%  Similarity=0.412  Sum_probs=40.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCC-EEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~-i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||.++++++|+++|..||. +..+.+       .++|||||+|.+
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~-------~~~g~afV~f~~   53 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-------LKSGYAFVDYPD   53 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-------EETTEEEECCSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-------cCCCEEEEEECC
Confidence            345689999999999999999999999998 554444       247999999975

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.40  E-value=1.1e-12  Score=73.79  Aligned_cols=55  Identities=16%  Similarity=0.285  Sum_probs=44.9

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ......++|||+|||+++++++|+++|..+|.|..+.++.++.+  ++|||||+|.+
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~   90 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFAR   90 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECC
Confidence            34455689999999999999999999999999999999887633  47999999976

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.40  E-value=1.3e-12  Score=71.13  Aligned_cols=48  Identities=23%  Similarity=0.220  Sum_probs=43.2

Q ss_pred             CCcEEEEecCC-CCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLT-YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~-~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+||| +.+++++|+++|..||.|.++.++.+     .+|||||+|.+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~   51 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMAD   51 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECC
Confidence            45899999999 89999999999999999999988764     37999999976

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.38  E-value=5.6e-13  Score=63.93  Aligned_cols=46  Identities=22%  Similarity=0.378  Sum_probs=41.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+++++++|+++|..+ .|..+.+.      +++|||||+|.+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~   49 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLN   49 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECC
Confidence            45899999999999999999999999 88888773      578999999975

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.38  E-value=1.7e-12  Score=72.96  Aligned_cols=54  Identities=22%  Similarity=0.231  Sum_probs=47.7

Q ss_pred             CCCcEEEEecCCCC-CCHHHHHHHhhccCCEEEEEEeecCC-CCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRF-TRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~i~~~~~~~~~~-~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||.. +++++|+++|..||.|..+.++.+.. |+.++|||||+|.+
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~  263 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFEN  263 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESS
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCC
Confidence            34589999999999 99999999999999999999988865 59999999999976

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.38  E-value=3e-12  Score=65.78  Aligned_cols=50  Identities=26%  Similarity=0.364  Sum_probs=42.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccE-EEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGF-AFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~-~fv~f~~   64 (65)
                      +.....|||+||++.+++++|+++|+.||.|.++.+...     .+|+ |||+|++
T Consensus        25 ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~   75 (130)
T 3zzy_A           25 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYAD   75 (130)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESC
T ss_pred             CCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECC
Confidence            344468999999999999999999999999999987653     3677 9999975

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.37  E-value=5.3e-12  Score=61.37  Aligned_cols=48  Identities=27%  Similarity=0.251  Sum_probs=41.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|+  ++++++|+++|..||.|..+.+.      +++|||||+|.+
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~   58 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEK   58 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESS
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECC
Confidence            3445689999995  89999999999999999998873      568999999975

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.36  E-value=3.3e-12  Score=67.11  Aligned_cols=50  Identities=26%  Similarity=0.462  Sum_probs=43.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||..+++++|+++|+.+|.|..+     ..++.++|||||+|.+
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~  145 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKS  145 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSS
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECC
Confidence            3455899999999999999999999999988654     4688999999999975

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.35  E-value=1.4e-12  Score=70.92  Aligned_cols=50  Identities=10%  Similarity=0.086  Sum_probs=43.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCE--EEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEV--GDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i--~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||+.+++++|+++|+.+|.|  ..+.+..+.  +..+|+|||+|.+
T Consensus       123 ~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~  174 (205)
T 3tyt_A          123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDS  174 (205)
T ss_dssp             CSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSS
T ss_pred             cceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCC
Confidence            4689999999999999999999999998  788877664  5567999999976

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.34  E-value=1.2e-11  Score=63.06  Aligned_cols=45  Identities=33%  Similarity=0.406  Sum_probs=39.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccE-EEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGF-AFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~-~fv~f~~   64 (65)
                      ..|||+||++.+++++|+++|+.||.|.++.+.. +     .|| |||+|++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~   71 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFES   71 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESS
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECC
Confidence            4678999999999999999999999999998754 2     286 9999975

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.34  E-value=1.3e-13  Score=72.57  Aligned_cols=55  Identities=18%  Similarity=0.149  Sum_probs=45.2

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..+|.+.. ..+.+..+++++|||||+|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~   63 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFES   63 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESS
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECC
Confidence            4556699999999999999999999999886544 234444688899999999976

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.32  E-value=4.8e-12  Score=70.57  Aligned_cols=48  Identities=42%  Similarity=0.711  Sum_probs=42.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+++++++|+++|..||.|..+.+..      ++|||||+|.+
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~   67 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLES   67 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECC
Confidence            4457999999999999999999999999999988753      47999999975

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.31  E-value=6.9e-12  Score=70.26  Aligned_cols=54  Identities=19%  Similarity=0.126  Sum_probs=48.6

Q ss_pred             CCCCcEEEEecCCCCC-CHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRT-TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~-~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||..+ ++++|+++|+.||.|..+.++.++ +|.++|+|||+|.+
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~  235 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYET  235 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSS
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCC
Confidence            3456899999999995 999999999999999999988886 89999999999976

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.31  E-value=1.7e-11  Score=68.65  Aligned_cols=49  Identities=20%  Similarity=0.161  Sum_probs=43.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||..+++++|+++|..||.|.++.++.++     +|||||+|.+
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~  253 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDN  253 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCC
Confidence            345889999999999999999999999999999887543     5899999976

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.29  E-value=3.5e-12  Score=68.27  Aligned_cols=47  Identities=30%  Similarity=0.345  Sum_probs=42.8

Q ss_pred             CcEEEEecCCC-CCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||. .+++++|+++|..+|.|..+.++.++     +|||||+|.+
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~   50 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMAD   50 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTT
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECC
Confidence            47999999999 99999999999999999999887754     7899999976

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.28  E-value=7.3e-12  Score=69.82  Aligned_cols=49  Identities=22%  Similarity=0.311  Sum_probs=43.2

Q ss_pred             CCCCcEEEEecCCCCC---------CHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRT---------TPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~---------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+||+..+         ++++|++.|+.||.|..+.++.      ++|||||.|.+
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~  188 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKY  188 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESS
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCC
Confidence            3456899999999998         6999999999999999998875      47999999975

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.23  E-value=2e-11  Score=70.95  Aligned_cols=48  Identities=29%  Similarity=0.493  Sum_probs=40.9

Q ss_pred             CCCcEEEEec--CCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDN--LTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~--l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.+.+|||+|  |++.+++++|++.|++||.|.++.+..      +||||||+|++
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~   65 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRT   65 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESS
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECC
Confidence            4458999998  588999999999999999998876532      57999999975

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.22  E-value=4.6e-11  Score=63.64  Aligned_cols=47  Identities=23%  Similarity=0.366  Sum_probs=39.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcc----C-------CEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERC----G-------EVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+++++++|+++|..+    |       .|..+.+      +.++|||||+|.+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~   60 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRS   60 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESC
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCC
Confidence            45899999999999999999999999    5       5555543      4568999999986

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.20  E-value=1.6e-10  Score=57.26  Aligned_cols=53  Identities=13%  Similarity=0.068  Sum_probs=43.9

Q ss_pred             CCcEEEEecCCC-----CCCHHHHHHHhhccCCEEEEEEeecCCC-CCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTY-----RTTPDDLRRVFERCGEVGDIYIPRDRFT-RESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~-----~~~~~~l~~~f~~~g~i~~~~~~~~~~~-~~~~g~~fv~f~~   64 (65)
                      .+++|++.|+..     +-.+++|++.|++||.|.++.++.++.+ +.++|++||+|.+
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~   65 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFER   65 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESS
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECC
Confidence            357999999963     2367899999999999999999888654 6889999999975

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.20  E-value=7e-11  Score=61.74  Aligned_cols=47  Identities=23%  Similarity=0.386  Sum_probs=39.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcc----C-------CEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERC----G-------EVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||.++++++|+++|+.+    |       .+..+.+.      .++|||||+|.+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~   60 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRS   60 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESS
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCC
Confidence            46899999999999999999999999    6       66666543      457999999975

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.15  E-value=8.7e-10  Score=54.28  Aligned_cols=50  Identities=24%  Similarity=0.278  Sum_probs=39.0

Q ss_pred             CCCCcEEEEecCC-------CCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLT-------YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~-------~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++-|.-..       ..+++++|+++|.+||.|..+.++     ++++|||||+|.+
T Consensus         7 ~~~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~   63 (100)
T 2d9o_A            7 GQGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFAT   63 (100)
T ss_dssp             CCSSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESC
T ss_pred             CCccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECC
Confidence            3344566665332       457899999999999999999876     4688999999975

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.14  E-value=2.6e-10  Score=55.75  Aligned_cols=42  Identities=33%  Similarity=0.423  Sum_probs=35.1

Q ss_pred             CcE-EEEecCCCCCCHHH----HHHHhhcc-CCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVS-LKVDNLTYRTTPDD----LRRVFERC-GEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~-l~v~~l~~~~~~~~----l~~~f~~~-g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+ |||+|||+.+++++    |+++|.+| |.|.++       ++   |+|||.|.+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~   55 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFIN   55 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESS
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECC
Confidence            345 99999999999877    66899999 499876       33   999999975

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.10  E-value=2.1e-10  Score=61.32  Aligned_cols=47  Identities=19%  Similarity=0.333  Sum_probs=42.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccC-CEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+|||+|||..+++++|+++|..+| .|..+.++.+     .+|+|||+|.+
T Consensus       120 ~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~  167 (198)
T 1qm9_A          120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGS  167 (198)
T ss_dssp             CCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSS
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCC
Confidence            58899999999999999999999999 9999887553     37999999976

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.10  E-value=4.6e-10  Score=61.51  Aligned_cols=47  Identities=19%  Similarity=0.333  Sum_probs=41.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccC-CEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCG-EVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||..+++++|+++|..+| .|..+.++..     .+|+|||+|.+
T Consensus       151 ~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~  198 (229)
T 2adc_A          151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGS  198 (229)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESS
T ss_pred             CCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECC
Confidence            58899999999999999999999999 9999887542     36899999976

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.00  E-value=3e-09  Score=52.87  Aligned_cols=53  Identities=21%  Similarity=0.295  Sum_probs=41.1

Q ss_pred             CCCCCCcEEEEecCCCCCC-----------HHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTT-----------PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~-----------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+...++|++.||.....           +++|+++|.+||.|..+.+ .++   .++|||||+|.+
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~   73 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRD   73 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSC
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECC
Confidence            3455568999999944432           4799999999999999955 443   379999999975

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.89  E-value=5.5e-09  Score=53.04  Aligned_cols=50  Identities=20%  Similarity=0.077  Sum_probs=43.9

Q ss_pred             CCCCCcEEEEecCCCC-CCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .-..++-|+|+||+.. +++++|++.|+.+|.|..+.++.+..      .|||+|.+
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~   64 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKE   64 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECC
Confidence            4566789999999999 99999999999999999999877654      38999976

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=98.89  E-value=3.9e-10  Score=55.71  Aligned_cols=46  Identities=17%  Similarity=0.322  Sum_probs=35.6

Q ss_pred             EecCCCCCCHHHHHHHh------------hccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          18 VDNLTYRTTPDDLRRVF------------ERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        18 v~~l~~~~~~~~l~~~f------------~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+|++.+++++|++.|            ++||.|.++.++.+. +++++|||||+|.+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~   77 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRR   77 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECC
Confidence            34555666666666555            999999999998875 57899999999976

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=98.79  E-value=2e-08  Score=49.64  Aligned_cols=52  Identities=25%  Similarity=0.215  Sum_probs=41.2

Q ss_pred             CcEEEEecC--CCCCC--------HHHHHHHhhccCCEEEEEEeecCCC--CCcccEEEEEEee
Q psy7053          13 MVSLKVDNL--TYRTT--------PDDLRRVFERCGEVGDIYIPRDRFT--RESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l--~~~~~--------~~~l~~~f~~~g~i~~~~~~~~~~~--~~~~g~~fv~f~~   64 (65)
                      ++.|.+.|+  |....        +++|++.|++||.|.++.++.++.+  +.++|++||+|.+
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~   68 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTS   68 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESS
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECC
Confidence            477888887  33332        3689999999999999999887654  4678999999975

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.70  E-value=4.1e-08  Score=49.48  Aligned_cols=53  Identities=13%  Similarity=0.167  Sum_probs=42.3

Q ss_pred             CCcEEEEecCCC--CC---CHHHHHHHhhccCCEEEEEEeecCC----CCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTY--RT---TPDDLRRVFERCGEVGDIYIPRDRF----TRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~--~~---~~~~l~~~f~~~g~i~~~~~~~~~~----~~~~~g~~fv~f~~   64 (65)
                      .++.|++.|+-.  +.   -+++|++.|++||.|.++.++.++.    ++.++|++||+|.+
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~   80 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSI   80 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESS
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECC
Confidence            357899999832  22   2589999999999999999988754    45678999999975

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.14  E-value=2.1e-06  Score=42.97  Aligned_cols=48  Identities=21%  Similarity=0.363  Sum_probs=35.6

Q ss_pred             CcEEEEecCCCCCC----------HHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTT----------PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~----------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++.|.+.|+=....          +++|++.|++||.|.++.+..+.    .+|++||+|.+
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~   64 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPS   64 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSS
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECC
Confidence            46788887622211          25789999999999998875542    58999999975

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=97.93  E-value=2.6e-05  Score=42.40  Aligned_cols=39  Identities=15%  Similarity=0.176  Sum_probs=32.4

Q ss_pred             CHHHHHHHhhccCCEEEEEEeec----CCCCCcccEEEEEEee
Q psy7053          26 TPDDLRRVFERCGEVGDIYIPRD----RFTRESRGFAFVRLLL   64 (65)
Q Consensus        26 ~~~~l~~~f~~~g~i~~~~~~~~----~~~~~~~g~~fv~f~~   64 (65)
                      .++++.+.|..||.|..+.+..+    +.++.++|++||+|.+
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~  184 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSI  184 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESS
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECC
Confidence            45789999999999999988744    3556899999999975

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.27  E-value=0.0017  Score=32.52  Aligned_cols=49  Identities=12%  Similarity=0.066  Sum_probs=41.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcc-----CCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERC-----GEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~-----g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+..+++-+-|||..+++..++.+..++     |.+.++.++.|.      +-|+|+|.+
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d   71 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRD   71 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSC
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEcc
Confidence            3446889999999999999999999999     999999887764      458899875

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.18  E-value=0.0022  Score=30.95  Aligned_cols=44  Identities=25%  Similarity=0.223  Sum_probs=32.6

Q ss_pred             CcEEEEecCCC----C-CCH---HHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTY----R-TTP---DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~----~-~~~---~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..||+|.-.+.    . .++   .+|.+.|.+||.+..++++.++        +||+|..
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d   58 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLE   58 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESS
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECC
Confidence            36788876652    2 232   5788999999999999988764        7999964

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.60  E-value=0.0095  Score=29.21  Aligned_cols=41  Identities=24%  Similarity=0.265  Sum_probs=32.2

Q ss_pred             EEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        16 l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |+.-+.|......+|.++|++||.+ .+.++-|-       -|||.|.+
T Consensus         8 V~~l~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~   48 (101)
T 3ctr_A            8 VLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQ   48 (101)
T ss_dssp             EEEEECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEE
T ss_pred             EEEEeCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecC
Confidence            4444999999999999999999954 77787762       47777764

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.55  E-value=0.018  Score=28.16  Aligned_cols=42  Identities=29%  Similarity=0.339  Sum_probs=32.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .-+++ +.|......+|.++|++||.+ .+.++-|-       -|||.|.+
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~   58 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQ   58 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSC
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecC
Confidence            34555 999999999999999999965 67777652       46776654

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.12  E-value=0.0099  Score=28.88  Aligned_cols=44  Identities=11%  Similarity=0.104  Sum_probs=33.5

Q ss_pred             CcEEEEecCCCC------CCH---HHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYR------TTP---DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~------~~~---~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..||+|.-++..      .++   .+|.+.|..||.+..++++.++        +||+|..
T Consensus        15 D~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d   67 (95)
T 1ufw_A           15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFAD   67 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSC
T ss_pred             CCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcC
Confidence            478999887632      332   4688899999999888888864        8999864

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=95.94  E-value=0.047  Score=26.20  Aligned_cols=51  Identities=10%  Similarity=0.040  Sum_probs=37.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCc--ccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRES--RGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~--~g~~fv~f~~   64 (65)
                      .+|-|..||...+++.+.+.+.....+.....+....+.+.  ..-|||.|.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~   54 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKN   54 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESS
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCC
Confidence            47899999999999999999998877776666554433332  2567888754

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.58  E-value=0.015  Score=35.40  Aligned_cols=47  Identities=6%  Similarity=0.175  Sum_probs=34.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+.|+|. .|...++.+|.+.|+.+|.|..+.+-.+  .   .-|+.|+|.+
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~--~---g~~~~vef~~   98 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES--F---GLYAVVEFCQ   98 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS--S---SEEEEEECC-
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc--C---CeEEEEEeCC
Confidence            34789997 7999999999999999999988765432  2   2599999974

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=92.01  E-value=0.19  Score=24.39  Aligned_cols=52  Identities=8%  Similarity=-0.023  Sum_probs=33.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCc--ccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRES--RGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~--~g~~fv~f~~   64 (65)
                      +-+|-|+.||...+++.+.+.+...-.+.....+....+.+.  -.-|||.|.+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~   62 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRN   62 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESC
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCC
Confidence            357899999999999999988887655544333322222211  1456777753

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=90.72  E-value=0.83  Score=22.47  Aligned_cols=45  Identities=20%  Similarity=0.067  Sum_probs=33.2

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhc-----cCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFER-----CGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~-----~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|.|.|+|..+.++.|.-+|+.     -|.+..+..  .+      +-|+|.|..
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~--~~------~~AvItF~d   56 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQR--LG------CGGVLTFRE   56 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEE--ET------TEEEEEESS
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEE--cC------CcEEEEEcC
Confidence            3489999999999999999999986     245655543  21      457888853

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	65
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-09
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-07
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-07
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	6e-07
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-06
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-06
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-06
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-06
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	8e-06
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-05
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-05
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 8e-05
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	9e-05
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	9e-05
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-04
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-04
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-04
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-04
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-04
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-04
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-04
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-04
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	9e-04
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.001
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.001
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.002
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	0.002
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	0.003

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.2 bits (112), Expect = 1e-09
 Identities = 17/46 (36%), Positives = 22/46 (47%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          SL V +L    T   L   F   G +  I + RD  TR S G+A+V
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 47

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.1 bits (109), Expect = 4e-09
 Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 8  PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-FTRESRGFAFVR 61
          P+ +    + V N+ ++    ++R +F   GE+  + +P+    T   RGF FV 
Sbjct: 3  PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 57

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (98), Expect = 1e-07
 Identities = 16/44 (36%), Positives = 22/44 (50%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          V  L+  T  + +R  F   GEV  I +P D  T + RGF F+ 
Sbjct: 4  VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFIT 47

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 41.9 bits (98), Expect = 1e-07
 Identities = 19/47 (40%), Positives = 24/47 (51%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          +L V NL    T D L  +F + G +    I RD+ T   RG AFVR
Sbjct: 8  NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 54

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.1 bits (96), Expect = 3e-07
 Identities = 19/52 (36%), Positives = 28/52 (53%)

Query: 10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          ++    L V  L ++TT  DL+  F   GEV  + + +D  T  S+GF FVR
Sbjct: 5  VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVR 56

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.3 bits (94), Expect = 4e-07
 Identities = 18/44 (40%), Positives = 27/44 (61%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          +  L+++TT + LR  F + GEV +  + RD  T+ SRGF FV 
Sbjct: 5  IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVT 48

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.0 bits (93), Expect = 6e-07
 Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 5/59 (8%)

Query: 2  SYGRPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          S G+P P I     +KV N+ +  + D++   F     +      +        G A V
Sbjct: 3  SSGKPGPTI-----IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 56

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (92), Expect = 8e-07
 Identities = 18/43 (41%), Positives = 24/43 (55%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +  L++ TT  DL+  F + GEV D  +  D  T  SRGF FV
Sbjct: 4  IGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFV 46

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 2e-06
 Identities = 19/56 (33%), Positives = 30/56 (53%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          R     E    L +  L++ TT + LR  +E+ G++ D  + RD  ++ SRGF FV
Sbjct: 12 RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFV 67

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (92), Expect = 2e-06
 Identities = 17/42 (40%), Positives = 25/42 (59%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAF 59
          +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF F
Sbjct: 11 IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGF 52

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (91), Expect = 4e-06
 Identities = 17/45 (37%), Positives = 24/45 (53%)

Query: 16  LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           + V  +   T    LR  FE+ G++  I I  DR + + RGFAFV
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 144

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 4e-06
 Identities = 13/43 (30%), Positives = 20/43 (46%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L    T  +L ++F + G +    I  D+ T  SRG  F+
Sbjct: 11 VSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFI 53

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 4e-06
 Identities = 17/46 (36%), Positives = 24/46 (52%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          ++    L  R  P DL   F   G+V D+ I  DR +R S+G A+V
Sbjct: 20 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 65

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 8e-06
 Identities = 18/44 (40%), Positives = 26/44 (59%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          +  L++ TT + LR  FE+ G + D  + RD  T+ SRGF FV 
Sbjct: 11 IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 54

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.7 bits (82), Expect = 4e-05
 Identities = 14/46 (30%), Positives = 27/46 (58%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +L V NL++ TT + +  +F + G++  I +  D+  + + GF FV
Sbjct: 9  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFV 54

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (81), Expect = 4e-05
 Identities = 9/43 (20%), Positives = 18/43 (41%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          +  L      D ++ +    G +    + +D  T  S+G+AF 
Sbjct: 6  IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 48

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 8e-05
 Identities = 6/48 (12%), Positives = 18/48 (37%), Gaps = 1/48 (2%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRL 62
           +++         +    + E+ GEV ++ +  +       G  +V+ 
Sbjct: 29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKF 75

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 9e-05
 Identities = 19/55 (34%), Positives = 33/55 (60%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          P  R +   +++V NL+  T   DL+ +F   G +  IY+ +D+ T +S+GFAF+
Sbjct: 1  PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 55

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.9 bits (80), Expect = 9e-05
 Identities = 5/36 (13%), Positives = 16/36 (44%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRF 50
          ++    +    T   +R+ F   G++ +I +  ++ 
Sbjct: 20 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG 55

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 1e-04
 Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 5/57 (8%)

Query: 5  RPPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          R PP  E    L + NL Y+ T +++  +F + G +  I +     TR   G A+V 
Sbjct: 1  RLPP--EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVV 52

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.3 bits (78), Expect = 1e-04
 Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 1/44 (2%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIY-IPRDRFTRESRGFAFV 60
          + NL        L   F   G +     I RD  T  S+G+AF+
Sbjct: 3  IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFI 46

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 33.8 bits (77), Expect = 2e-04
 Identities = 12/40 (30%), Positives = 17/40 (42%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRES 54
          +L V+ L    T  +L  +F   G +    I RD  T  S
Sbjct: 4  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYS 43

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.2 bits (78), Expect = 2e-04
 Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 5/61 (8%)

Query: 6  PPPR---IEGMVSLK--VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           P     +  MV  +  +D+  Y    +D+R    + G V  I IPR     E  G   +
Sbjct: 2  HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKI 61

Query: 61 R 61
           
Sbjct: 62 F 62

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.5 bits (76), Expect = 3e-04
 Identities = 22/46 (47%), Positives = 28/46 (60%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
           L V  L+  TT  DLR VF + G + D+ I  D+ +R SRGFAFV
Sbjct: 11 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 56

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.5 bits (76), Expect = 3e-04
 Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 3/46 (6%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGD---IYIPRDRFTRESRGFAFV 60
          + NL + TT + L+ VF + G +                S GF FV
Sbjct: 3  IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFV 48

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.8 bits (77), Expect = 3e-04
 Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 4/44 (9%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          V+NL Y  T D L ++F + G V  I      FT+ ++  A ++
Sbjct: 12 VENLFYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALLQ 51

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 32.6 bits (74), Expect = 4e-04
 Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          L V NL +  +  D++ +F   G +    +     +  S G A V
Sbjct: 3  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHY-DRSGRSLGTADV 46

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.7 bits (74), Expect = 6e-04
 Identities = 13/46 (28%), Positives = 26/46 (56%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          ++ V  L  + +   L  +F + G V + ++P+DR T + +G+ FV
Sbjct: 11 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFV 56

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 32.0 bits (72), Expect = 9e-04
 Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 6  PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          P   +EG + L V ++      D+++  F   GE+ +I++  DR T  S+G+A V
Sbjct: 1  PQRSVEGWI-LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 54

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.1 bits (73), Expect = 0.001
 Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 10/60 (16%)

Query: 2  SYGRPPPRIEGMVSLKVDNL-TYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          S G+  PR      + + NL T      D+  +F + G++    +         +GFAFV
Sbjct: 5  SSGKTDPRSMN-SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFV 55

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.0 bits (72), Expect = 0.001
 Identities = 8/48 (16%), Positives = 17/48 (35%), Gaps = 5/48 (10%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPR-----DRFTRESRGFAFV 60
          V N+ +  T + +   F     +G +              + + FAF+
Sbjct: 6  VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFL 53

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 31.4 bits (71), Expect = 0.002
 Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 7/55 (12%)

Query: 10 IEGMVS---LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVR 61
          I+ M      + D L      +DLR    + G++  + +          G A V 
Sbjct: 13 IKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHP----DGVASVS 63

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 31.2 bits (70), Expect = 0.002
 Identities = 17/43 (39%), Positives = 20/43 (46%)

Query: 18 VDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFV 60
          V  L        L   F   G++ DI IP D  T + RGFAFV
Sbjct: 10 VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 52

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 30.9 bits (69), Expect = 0.003
 Identities = 10/41 (24%), Positives = 14/41 (34%)

Query: 15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESR 55
          ++ V  L    T DDL   F++CG V               
Sbjct: 10 AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYL 50

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	65
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.82
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.81
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.81
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.8
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.8
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.79
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.79
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.79
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.79
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.79
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.79
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.79
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.78
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.78
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.78
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.78
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.77
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.77
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.77
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.76
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.75
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.74
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.71
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.71
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.7
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.69
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.69
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.69
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.69
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.68
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.67
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.67
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.67
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.66
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.66
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.65
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.64
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.64
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.64
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.64
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.62
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.59
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.59
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.58
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.58
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.58
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.58
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.58
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.57
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.57
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.57
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.57
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.57
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.55
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.55
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.52
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.52
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.5
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.5
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.5
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.49
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.49
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.49
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.47
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.47
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.46
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.46
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.41
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.41
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.38
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.37
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.37
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.32
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.3
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.24
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	98.99
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.91
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.63
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.37
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.47
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	87.88

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.6e-20  Score=89.22  Aligned_cols=56  Identities=36%  Similarity=0.547  Sum_probs=52.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +++..++|||+|||+++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+
T Consensus         2 epe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~   57 (84)
T d1l3ka1           2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT   57 (84)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCCCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcC
Confidence            45566899999999999999999999999999999999999999999999999975

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=3.7e-20  Score=88.96  Aligned_cols=55  Identities=35%  Similarity=0.506  Sum_probs=51.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+..++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~   59 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE   59 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESS
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECC
Confidence            4456899999999999999999999999999999999999999999999999975

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=3e-20  Score=86.72  Aligned_cols=51  Identities=31%  Similarity=0.477  Sum_probs=48.7

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEeeC
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF   65 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~   65 (65)
                      +|||+|||+++++++|+++|+.||.|.++.++.++.+++++|||||+|.+.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~   51 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE   51 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSS
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCH
Confidence            589999999999999999999999999999999999999999999999863

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.81  E-value=1.2e-19  Score=86.70  Aligned_cols=58  Identities=28%  Similarity=0.340  Sum_probs=52.8

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |.+..++++|||+|||.++++++|+++|+.+|.|.+++++.++.+|+++|||||+|.+
T Consensus         1 P~~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~   58 (88)
T d1rk8a_           1 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET   58 (88)
T ss_dssp             CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECC
Confidence            4455667899999999999999999999999999999999999999999999999976

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.6e-19  Score=87.09  Aligned_cols=58  Identities=24%  Similarity=0.394  Sum_probs=52.9

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+.+..++|||+|||.++++++|+++|+.+|.|.++.++.++.++.++|||||+|.+
T Consensus         3 ~~~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~   60 (93)
T d1x5ua1           3 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS   60 (93)
T ss_dssp             CCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESS
T ss_pred             CCcCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECC
Confidence            3455556899999999999999999999999999999999999999999999999975

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=4e-19  Score=87.02  Aligned_cols=55  Identities=33%  Similarity=0.518  Sum_probs=50.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||+.+++++|+++|+.||.|.++.++.++.+|+++|||||+|.+
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~   61 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD   61 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESS
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECC
Confidence            3344789999999999999999999999999999999999999999999999975

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.6e-19  Score=84.13  Aligned_cols=50  Identities=36%  Similarity=0.544  Sum_probs=48.2

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +|||+|||+++++++|++.|+.+|.|..+.++.++.+++++|||||+|.+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~   50 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKE   50 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESS
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECC
Confidence            58999999999999999999999999999999999999999999999986

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.9e-19  Score=85.65  Aligned_cols=57  Identities=32%  Similarity=0.614  Sum_probs=52.5

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++.+...+|||+|||.++++++|+++|+.||.|.++.++.++.++.++|||||+|.+
T Consensus         3 ~~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~   59 (90)
T d2cq0a1           3 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR   59 (90)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESS
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECC
Confidence            445566899999999999999999999999999999999998899999999999976

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=5.3e-20  Score=86.24  Aligned_cols=51  Identities=35%  Similarity=0.652  Sum_probs=48.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++|||+|||+++++++|++.|+.+|.|.++.++.++.+|+++|||||+|.+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~   51 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD   51 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECC
Confidence            579999999999999999999999999999999999999999999999986

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.79  E-value=5.3e-19  Score=83.94  Aligned_cols=54  Identities=35%  Similarity=0.452  Sum_probs=50.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||+++++++|+++|+.+|.|.+++++.++.+++++|||||+|.+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~   57 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK   57 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECC
Confidence            345789999999999999999999999999999999999999999999999986

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=6.5e-20  Score=89.96  Aligned_cols=52  Identities=33%  Similarity=0.586  Sum_probs=49.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~   71 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS   71 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECC
Confidence            4799999999999999999999999999999999999999999999999976

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=4.7e-19  Score=83.75  Aligned_cols=54  Identities=41%  Similarity=0.554  Sum_probs=50.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +..++|||+|||+++++++|+++|+.+|.|.++.++.++.+++++|||||+|.+
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~   60 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN   60 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECC
Confidence            345799999999999999999999999999999999999999999999999986

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=5.6e-19  Score=83.92  Aligned_cols=53  Identities=28%  Similarity=0.367  Sum_probs=50.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.++|||+|||..+++++|+++|++||.|.++.++.++.+|.++|||||+|.+
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~   57 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDK   57 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcC
Confidence            34789999999999999999999999999999999999899999999999976

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=7.5e-19  Score=84.69  Aligned_cols=55  Identities=25%  Similarity=0.543  Sum_probs=51.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+.+++|||+|||+++++++|+++|+.+|.|.++.++.++.++.++|||||+|.+
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~   58 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYS   58 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECC
Confidence            3556899999999999999999999999999999999999999999999999976

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.8e-19  Score=87.41  Aligned_cols=52  Identities=33%  Similarity=0.487  Sum_probs=49.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||+++++++|+++|..||.|.++.++.+..+|+++|||||+|.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~   69 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE   69 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECC
Confidence            4789999999999999999999999999999999999999999999999976

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=1.2e-18  Score=84.71  Aligned_cols=54  Identities=33%  Similarity=0.695  Sum_probs=50.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+|||+|||+.+++++|+++|..+|.|.++.++.++.+++++|||||+|.+
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~   59 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMF   59 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESS
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECC
Confidence            445789999999999999999999999999999999999999999999999976

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=1.1e-18  Score=84.42  Aligned_cols=58  Identities=19%  Similarity=0.387  Sum_probs=53.1

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |...++.++|||+|||+++++++|+++|..+|.+..+.+..+..++.++|||||+|.+
T Consensus         2 P~~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~   59 (98)
T d1x4ha1           2 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMT   59 (98)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESS
T ss_pred             ccCCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcC
Confidence            4456667899999999999999999999999999999999998899999999999975

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=1e-18  Score=82.12  Aligned_cols=51  Identities=33%  Similarity=0.407  Sum_probs=48.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+|||+|||+.+++++|+++|+.+|.|.+++++.++.+|+++|||||+|.+
T Consensus         1 aslfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~   51 (80)
T d1cvja1           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ   51 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECC
Confidence            369999999999999999999999999999999999999999999999975

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=9.7e-19  Score=85.48  Aligned_cols=56  Identities=23%  Similarity=0.165  Sum_probs=51.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.+.+++|||+|||+++++++|+++|..||.+..+.++.++.+|.++|||||+|.+
T Consensus        14 ~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~   69 (102)
T d2cpza1          14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN   69 (102)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCC
Confidence            33455789999999999999999999999999999999999999999999999976

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.77  E-value=7.9e-19  Score=82.73  Aligned_cols=52  Identities=31%  Similarity=0.349  Sum_probs=49.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||.++++++|+++|+.+|.|..+.++.++.+|+++|||||+|.+
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~   53 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTS   53 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECC
Confidence            4689999999999999999999999999999999998999999999999986

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=8.7e-19  Score=83.25  Aligned_cols=52  Identities=19%  Similarity=0.328  Sum_probs=49.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEeeC
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF   65 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~   65 (65)
                      .+|||+|||+++++++|+++|+.+|.|.++.++.++.+|+++|||||+|.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~   53 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI   53 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSS
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCH
Confidence            4799999999999999999999999999999999999999999999999763

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.77  E-value=1.5e-18  Score=88.56  Aligned_cols=55  Identities=33%  Similarity=0.517  Sum_probs=50.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+..++|||+|||+++++++|+++|+.||.|.++.++.++.+++++|||||+|.+
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~   93 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS   93 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECC
Confidence            3445789999999999999999999999999999999999999999999999986

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=3.6e-19  Score=85.18  Aligned_cols=53  Identities=36%  Similarity=0.451  Sum_probs=50.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+++++++|+++|+.+|.|..+.++.++.+++++|||||+|.+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~   56 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL   56 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECC
Confidence            34799999999999999999999999999999999999999999999999975

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=2.1e-18  Score=83.21  Aligned_cols=56  Identities=23%  Similarity=0.528  Sum_probs=50.1

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecC-CCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-FTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~-~~~~~~g~~fv~f~~   64 (65)
                      +.....+|||+|||+++++++|+++|..||.|..+.++.+. .+|+++|||||+|.+
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~   60 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT   60 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECC
Confidence            34455889999999999999999999999999999998875 489999999999986

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2.3e-18  Score=80.64  Aligned_cols=52  Identities=33%  Similarity=0.422  Sum_probs=49.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||+++++++|+++|+.+|.+..+.+..++.+++++|||||+|.+
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~   53 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD   53 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcC
Confidence            4799999999999999999999999999999999999999999999999976

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.2e-19  Score=87.94  Aligned_cols=53  Identities=26%  Similarity=0.466  Sum_probs=49.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+++++++|+++|+.||.|.++.++.++.+|+++|||||+|.+
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~   59 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD   59 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSC
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECC
Confidence            34789999999999999999999999999999999999999999999999975

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=4.7e-18  Score=79.97  Aligned_cols=51  Identities=29%  Similarity=0.516  Sum_probs=48.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+|||+|||.++++++|+++|+.+|.|.++.++.+..+++++|||||+|.+
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~   53 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYID   53 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECC
Confidence            579999999999999999999999999999999998899999999999975

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=3.7e-18  Score=81.63  Aligned_cols=54  Identities=31%  Similarity=0.559  Sum_probs=50.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+.++|||+|||+++++++|+++|..+|.|..+.++.+..++.++|||||+|.+
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~   56 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN   56 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSS
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECC
Confidence            345789999999999999999999999999999999888899999999999975

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=3.3e-17  Score=77.73  Aligned_cols=51  Identities=24%  Similarity=0.283  Sum_probs=47.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||.++++++|+++|+.+|.|..+.+..+. +++++|||||+|.+
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~   56 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDS   56 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESC
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcC
Confidence            4799999999999999999999999999999988775 89999999999986

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=3.7e-17  Score=76.40  Aligned_cols=49  Identities=27%  Similarity=0.373  Sum_probs=46.4

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +|||+|||+++++++|+++|+.||.|.++.+..++ +++++|||||+|.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~   50 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFER   50 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECC
Confidence            69999999999999999999999999999998885 89999999999986

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.70  E-value=1.6e-17  Score=78.07  Aligned_cols=51  Identities=18%  Similarity=0.164  Sum_probs=41.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ++|||+|||+++++++|+++|+.+|.|..+.++.+..+|+++|||||+|.+
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~   52 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTS   52 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSS
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECC
Confidence            689999999999999999999999999888787777899999999999976

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=8.6e-17  Score=76.87  Aligned_cols=52  Identities=17%  Similarity=0.214  Sum_probs=46.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...++|||+|||.++++++|+++|+.+|.|.++.++.++.++  +|||||+|.+
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~   57 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYE   57 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECC
Confidence            345899999999999999999999999999999998876544  7999999986

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=2.1e-17  Score=76.54  Aligned_cols=50  Identities=34%  Similarity=0.538  Sum_probs=47.5

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +|||+|||+++++++|+++|+.+|.+..+.++.++.+++++|||||+|.+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~   50 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES   50 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECC
Confidence            58999999999999999999999999999998998899999999999976

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.2e-16  Score=79.01  Aligned_cols=51  Identities=29%  Similarity=0.447  Sum_probs=45.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +..++|||+|||..+++++|+++|+.||.|..+++..   ++.++|||||+|.+
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~   55 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYED   55 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECC
Confidence            3458999999999999999999999999999998765   45678999999975

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=6.1e-17  Score=74.54  Aligned_cols=49  Identities=24%  Similarity=0.348  Sum_probs=47.1

Q ss_pred             EEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        16 l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |||+|||.++++++|+++|..||.|..+.+..++.++.++|+|||+|.+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~   49 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDS   49 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECC
Confidence            7999999999999999999999999999999998999999999999986

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=3.2e-16  Score=76.21  Aligned_cols=54  Identities=26%  Similarity=0.381  Sum_probs=48.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||.++++++|+++|+.+|.|..+.+..+. ++.++|||||+|.+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~   68 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMES   68 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCC
Confidence            3445899999999999999999999999999999888774 88999999999986

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=3.8e-17  Score=77.02  Aligned_cols=49  Identities=27%  Similarity=0.332  Sum_probs=45.1

Q ss_pred             EEEecCCCCCCHHHHHHHhhccCCEEEE-EEeecCCCCCcccEEEEEEee
Q psy7053          16 LKVDNLTYRTTPDDLRRVFERCGEVGDI-YIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        16 l~v~~l~~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |||+|||+++++++|+++|+.+|.|.++ .++.++.+|+++|||||+|.+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~   50 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFAS   50 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSS
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECC
Confidence            7999999999999999999999998664 678888899999999999986

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=7.7e-17  Score=76.24  Aligned_cols=49  Identities=31%  Similarity=0.510  Sum_probs=44.3

Q ss_pred             EEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCC---CcccEEEEEEee
Q psy7053          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTR---ESRGFAFVRLLL   64 (65)
Q Consensus        16 l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~---~~~g~~fv~f~~   64 (65)
                      |||+|||+++++++|+++|+.||.|..+.++.++.++   .++|||||+|.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~   52 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKK   52 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECC
Confidence            7999999999999999999999999999998876555   468999999986

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.67  E-value=6.2e-17  Score=76.83  Aligned_cols=53  Identities=23%  Similarity=0.248  Sum_probs=43.8

Q ss_pred             CCcEEEEecCCCCCC-HHHHHHHhhccCCEEEEEEeec-CCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTT-PDDLRRVFERCGEVGDIYIPRD-RFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~-~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~g~~fv~f~~   64 (65)
                      +.++|||+|||++++ ++.|+++|+.||.|.++.++.+ ..+++++|||||+|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~   57 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFEN   57 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESS
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECC
Confidence            458999999999875 5679999999999999988764 5789999999999975

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=6.9e-16  Score=74.05  Aligned_cols=54  Identities=31%  Similarity=0.487  Sum_probs=47.0

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+++++++|+++|..+|.|..+.++.++  +.++|||||+|.+
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~   60 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFEN   60 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECC
Confidence            33445789999999999999999999999999999988875  3368999999986

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=2e-16  Score=76.68  Aligned_cols=56  Identities=30%  Similarity=0.288  Sum_probs=48.6

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEE--------EEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVG--------DIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.....+|||+|||+.+++++|+++|..||.|.        .+.+..++.+++++|||||+|.+
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~   67 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED   67 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSS
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecC
Confidence            445568999999999999999999999999773        45667777889999999999976

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=8.2e-16  Score=75.05  Aligned_cols=56  Identities=16%  Similarity=0.185  Sum_probs=48.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .......|||+|||+++++++|+++|..+|.+....++.+..+++++|+|||+|.+
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~   66 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFAS   66 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESS
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCC
Confidence            34455679999999999999999999999988876677777799999999999986

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=6e-16  Score=75.45  Aligned_cols=53  Identities=17%  Similarity=0.382  Sum_probs=45.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecC-CCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDR-FTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~-~~~~~~g~~fv~f~~   64 (65)
                      +..++|||+|||+++++++|+++|+.|| +..+.++.+. .+++++|||||+|.+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~   66 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED   66 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESS
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECC
Confidence            3458999999999999999999999998 6677776654 578999999999986

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=3.7e-16  Score=75.32  Aligned_cols=51  Identities=20%  Similarity=0.271  Sum_probs=46.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCC-EEEEEEeecC-CCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGE-VGDIYIPRDR-FTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~-i~~~~~~~~~-~~~~~~g~~fv~f~~   64 (65)
                      ++|||+|||..+++++|+++|+.+|. +..+.++.+. .+++++|||||+|.+
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~   54 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES   54 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESS
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcC
Confidence            68999999999999999999999995 8888888775 468999999999986

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=5.3e-16  Score=73.91  Aligned_cols=51  Identities=22%  Similarity=0.354  Sum_probs=45.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+|||+|||+++++++|+++|+.+|.|..+.++.+.  +.++|||||+|.+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~   57 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFET   57 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECC
Confidence            34689999999999999999999999999999998875  3478999999986

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.8e-16  Score=82.38  Aligned_cols=56  Identities=36%  Similarity=0.547  Sum_probs=51.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +++..++|||+|||+.+++++|+++|+.+|.|..+.++.+..++.++|||||+|.+
T Consensus         2 ep~~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~   57 (183)
T d1u1qa_           2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT   57 (183)
T ss_dssp             CCHHHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESS
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCC
Confidence            34556899999999999999999999999999999999998999999999999975

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.64  E-value=1.9e-17  Score=79.44  Aligned_cols=56  Identities=16%  Similarity=0.153  Sum_probs=48.2

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+....++|||+|||+++++++|+++|..+|.|..+.++.+ .+|+++|||||+|.+
T Consensus         8 ~~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~   63 (91)
T d1fjeb1           8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFES   63 (91)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESS
T ss_pred             CCCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCC
Confidence            34455679999999999999999999999998887776544 589999999999986

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=6.6e-17  Score=78.60  Aligned_cols=54  Identities=31%  Similarity=0.284  Sum_probs=48.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +..++|||+|||.++++++|+++|..+|.+..+.+..+..+|+++|||||+|.+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~   69 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPN   69 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEecc
Confidence            345899999999999999999999999998888777777789999999999976

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=7.1e-16  Score=76.19  Aligned_cols=56  Identities=14%  Similarity=0.132  Sum_probs=47.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.....+|||+|||+++++++|+++|..+|.+..+.++.+..+|.++|+|||+|.+
T Consensus        14 ~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~   69 (112)
T d1wela1          14 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN   69 (112)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSS
T ss_pred             CCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECC
Confidence            34456799999999999999999999999987665455556799999999999976

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=3.5e-15  Score=72.56  Aligned_cols=57  Identities=18%  Similarity=0.150  Sum_probs=47.4

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEeeC
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF   65 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~   65 (65)
                      ..+.....+|||+|||+++++++|+++|..+|. ..+.++.+. +++.+|||||+|.+.
T Consensus         9 ~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~   65 (102)
T d1weza_           9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATH   65 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSS
T ss_pred             CCcCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCH
Confidence            345556689999999999999999999999974 467677664 789999999999863

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.58  E-value=4.7e-15  Score=68.71  Aligned_cols=49  Identities=16%  Similarity=0.289  Sum_probs=43.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+|||+|||+++++++|+++|+.+|.|..+.++.++..  .++||||+|.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~   49 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFAR   49 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESS
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcc
Confidence            47999999999999999999999999999999887643  45799999975

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=9e-16  Score=74.73  Aligned_cols=52  Identities=15%  Similarity=0.093  Sum_probs=45.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+|||+|||+++++++|+++|..+|.+.....+....+|+++|+|||+|.+
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s   59 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKN   59 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSS
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECC
Confidence            4689999999999999999999999988765455555699999999999976

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=8.1e-15  Score=70.44  Aligned_cols=52  Identities=27%  Similarity=0.346  Sum_probs=44.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+..++|||+|||.++++++|+++|..+|.|..+.+..   ++.++|||||+|.+
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~---~~~~~g~afV~f~~   62 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFED   62 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc---cccccceEEEEECC
Confidence            45557899999999999999999999999998877644   45678999999986

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.4e-15  Score=72.34  Aligned_cols=48  Identities=38%  Similarity=0.587  Sum_probs=42.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||+.+++++|+++|..||.|.++.+.     ..++|||||+|.+
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~   51 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFAD   51 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECC
Confidence            45899999999999999999999999999888653     4468999999975

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=1.5e-15  Score=72.42  Aligned_cols=55  Identities=16%  Similarity=0.195  Sum_probs=46.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHH---HHHhhccCCEEEEEEeecCCCCCc---ccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDL---RRVFERCGEVGDIYIPRDRFTRES---RGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l---~~~f~~~g~i~~~~~~~~~~~~~~---~g~~fv~f~~   64 (65)
                      ..+..+|||+|||+.+++++|   .++|++||.|..+.++.++.++..   +|||||+|.+
T Consensus         5 viq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~   65 (89)
T d2cpia1           5 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR   65 (89)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESS
T ss_pred             EEecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEeccc
Confidence            345578999999999999999   668999999999999988766554   4899999986

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=2e-15  Score=74.07  Aligned_cols=49  Identities=24%  Similarity=0.373  Sum_probs=42.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....++|||+|||+.+++++|+++|..||.|..+.+.      ..+|||||+|.+
T Consensus         7 ~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~   55 (111)
T d1whxa_           7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLE   55 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcC
Confidence            3345789999999999999999999999999998763      357999999975

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.57  E-value=2.1e-15  Score=72.64  Aligned_cols=54  Identities=24%  Similarity=0.434  Sum_probs=45.3

Q ss_pred             CCCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           6 PPPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         6 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +.......++|||+|||+++++++|+++|..+|.+..+.     .+++++|||||+|.+
T Consensus         9 ~~~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~   62 (96)
T d1fjca_           9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKS   62 (96)
T ss_dssp             TTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESS
T ss_pred             ccCcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCC
Confidence            344556678999999999999999999999999875543     378899999999986

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.57  E-value=1.5e-15  Score=71.81  Aligned_cols=53  Identities=17%  Similarity=0.168  Sum_probs=44.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....|||+|||+++++++|+++|..+|.+.....+....+++++|+|||+|.+
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~   60 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES   60 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcC
Confidence            34789999999999999999999999987654344445689999999999986

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.57  E-value=1.2e-14  Score=68.27  Aligned_cols=47  Identities=19%  Similarity=0.205  Sum_probs=42.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||.++++++|..+|+.+|.|.+++++.+     .+|||||+|.+
T Consensus         8 ~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~   54 (83)
T d2b0ga1           8 NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTT   54 (83)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESS
T ss_pred             CCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCC
Confidence            489999999999999999999999999999988653     36899999986

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.6e-14  Score=75.62  Aligned_cols=56  Identities=30%  Similarity=0.353  Sum_probs=51.5

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....++|||+|||+.+++++|+++|..+|.|..+.++.++.+++++|||||+|.+
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~  148 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD  148 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESC
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECC
Confidence            34455899999999999999999999999999999999999899999999999986

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.2e-14  Score=70.10  Aligned_cols=47  Identities=19%  Similarity=0.384  Sum_probs=42.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||..+++++|+++|+.||.|.++.++.+      +|||||+|.+
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~   63 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFST   63 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESS
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECC
Confidence            3478999999999999999999999999999988764      6999999976

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=7.8e-15  Score=71.91  Aligned_cols=48  Identities=25%  Similarity=0.317  Sum_probs=43.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+|||+|||+.+++++|+++|+.||.|.++.+..++    .+|+|||+|.+
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~   54 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYAD   54 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECC
Confidence            4789999999999999999999999999999887653    57999999986

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=2.5e-14  Score=67.81  Aligned_cols=48  Identities=19%  Similarity=0.295  Sum_probs=41.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +++|||+|||.++++++|+++|+.+|.+.++....    ++.+|||||+|++
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~   57 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGS   57 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESS
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECC
Confidence            47999999999999999999999999987775543    4467999999986

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=7.9e-14  Score=67.35  Aligned_cols=51  Identities=22%  Similarity=0.321  Sum_probs=43.8

Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |+......+|||+|||+.+++++|+++|..+|.|..+.+..       +|||||+|.+
T Consensus         9 p~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~   59 (98)
T d1wg4a_           9 PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLR   59 (98)
T ss_dssp             CCCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESS
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECC
Confidence            44445568899999999999999999999999999987643       4899999986

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=4.2e-14  Score=69.13  Aligned_cols=47  Identities=30%  Similarity=0.345  Sum_probs=41.6

Q ss_pred             CcEEEEecCCC-CCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTY-RTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+|||+|||+ .+++++|+++|+.||.|..+.++.++     +|||||+|++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~   49 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMAD   49 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECC
Confidence            47899999965 58999999999999999999987753     6899999986

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.50  E-value=5.1e-14  Score=66.58  Aligned_cols=48  Identities=35%  Similarity=0.697  Sum_probs=42.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEeeC
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF   65 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~   65 (65)
                      +.++|||+|||.++++++|+++|+.||.|.++.+..+      +|||||+|++.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~   54 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETR   54 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCH
Confidence            3468999999999999999999999999999987653      68999999863

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.50  E-value=1.7e-13  Score=66.66  Aligned_cols=51  Identities=16%  Similarity=0.168  Sum_probs=44.3

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           8 PRIEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         8 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....+++|||+|||..+++++|.++|..||.|.++.+..      .+|+|||+|++
T Consensus        10 ~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~------~k~~AfV~f~~   60 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFEN   60 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESS
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe------cceeEEEEeCC
Confidence            3445568999999999999999999999999999987754      46899999976

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=1e-13  Score=65.69  Aligned_cols=49  Identities=18%  Similarity=0.186  Sum_probs=42.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+.+++|||+|||.++++++|.++|+++|.|..+.+..      .+|+|||+|.+
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~------~~~~afV~f~~   53 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK------GKNQAFLELAT   53 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEET------TTTEEEEEESS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccc------cceEEEEEeCC
Confidence            34458999999999999999999999999999987764      35899999986

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=2.8e-14  Score=67.61  Aligned_cols=43  Identities=21%  Similarity=0.253  Sum_probs=39.1

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      +|||+|||+.+++++|+++|+.+|.|.++.+..       .|||||+|.+
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~   44 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVR   44 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESS
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCC
Confidence            699999999999999999999999999988754       3899999976

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=1.2e-15  Score=72.69  Aligned_cols=52  Identities=17%  Similarity=0.270  Sum_probs=43.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEe-----ecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIP-----RDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~-----~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||+++++++|+++|+.+|.+..+.+.     .+..+++++|||||+|.+
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~   57 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS   57 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESS
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCC
Confidence            3789999999999999999999999876544332     344678899999999986

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=2.3e-14  Score=68.38  Aligned_cols=49  Identities=31%  Similarity=0.550  Sum_probs=41.3

Q ss_pred             CcEEEEecCCCCCCHHHHHH----HhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRR----VFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~----~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||+.+++++|++    +|+.||.|..+.+..   +++++|||||+|.+
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~   55 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKE   55 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECC
Confidence            47999999999999988754    578999998877643   67789999999986

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=7.9e-14  Score=67.37  Aligned_cols=46  Identities=22%  Similarity=0.415  Sum_probs=39.8

Q ss_pred             CCCcEEEEecCC-CCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLT-YRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~-~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ....+|||+||| ..+++.+|+++|.+||.|.++.+        ++|||||+|++
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~   59 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVN   59 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESS
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECC
Confidence            444789999996 57888999999999999999877        46999999986

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.46  E-value=1.9e-13  Score=65.76  Aligned_cols=46  Identities=26%  Similarity=0.350  Sum_probs=41.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||.++++++|+++|+.||.|..+.+..      .++||||+|.+
T Consensus        17 s~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~------~~~~afV~f~~   62 (97)
T d1whya_          17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK------GDSFAYIQYES   62 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECS------SSCCEEEEESS
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeec------cccEEEeccCC
Confidence            58999999999999999999999999999988754      36899999986

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=8e-14  Score=65.76  Aligned_cols=47  Identities=21%  Similarity=0.274  Sum_probs=40.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..++|||+|||.++++++|+++|+.+|.+..+.+      ++++|||||+|.+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~------~~~rg~afV~f~~   53 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSN   53 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE------EECSSEEEEEESS
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE------ccccEEEEEEeCC
Confidence            4478999999999999999999999998766654      3467999999976

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.41  E-value=6.6e-13  Score=65.46  Aligned_cols=48  Identities=21%  Similarity=0.185  Sum_probs=42.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .....+||||||..+++++|+++|+.||.|..+.++.      .+|+|||.|.+
T Consensus         9 ~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~------~kg~gfV~F~~   56 (113)
T d1owxa_           9 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR------GAKEGIILFKE   56 (113)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT------TCSEEEEEESS
T ss_pred             CCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEec------CCceEEEEecC
Confidence            3445679999999999999999999999999998864      36999999976

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=3.1e-13  Score=65.31  Aligned_cols=49  Identities=16%  Similarity=0.216  Sum_probs=42.2

Q ss_pred             CCCCcEEEEecCCCC-CCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          10 IEGMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        10 ~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+++|||+|||.+ +++++|.++|+.||.|..+.++.      .+|+|||+|.+
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~------~k~~afV~f~~   64 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMET   64 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSS
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEee------cCCcEEEEecc
Confidence            345589999999985 89999999999999999998764      35899999986

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=5.3e-13  Score=62.06  Aligned_cols=46  Identities=28%  Similarity=0.284  Sum_probs=39.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          11 EGMVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        11 ~~~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++++|||+|++  +++++|+++|++||.|.++.+..      .+|||||+|.+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~------~~~~afV~f~~   48 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEK   48 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET------TTTEEEEECSS
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeecc------CCCEEEEEEcc
Confidence            456899999986  89999999999999999987754      46899999975

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.37  E-value=8.3e-13  Score=62.70  Aligned_cols=50  Identities=16%  Similarity=0.208  Sum_probs=42.9

Q ss_pred             CCCCCcEEEEecCCCC-CCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           9 RIEGMVSLKVDNLTYR-TTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         9 ~~~~~~~l~v~~l~~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ..+.++.|||+|||.. +++++|.++|++||.|..+.+..+      +++|||+|++
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~   54 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMAT   54 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESS
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcc
Confidence            4466789999999986 789999999999999999988654      4689999986

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=1.2e-13  Score=64.48  Aligned_cols=45  Identities=29%  Similarity=0.266  Sum_probs=38.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+|||+|||.++++++|+++|..+|.+....+.      ..+|||||+|.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~------~~rg~aFV~f~~   46 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPD   46 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE------EETTEEEECCSC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEe------cccceEEEEECC
Confidence            479999999999999999999999987654443      357999999976

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=3.9e-13  Score=63.72  Aligned_cols=45  Identities=20%  Similarity=0.265  Sum_probs=37.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .++|||+|||+++++++|+++|..||. ..+.      .+..+|||||+|.+
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~------~~~~kg~afV~f~~   49 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYDL-KYCY------VDRNKRTAFVTLLN   49 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSCC-CCEE------EEGGGTEEEECCSC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcCc-eeee------eeccCCceEEEECC
Confidence            478999999999999999999999992 2222      24568999999976

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.30  E-value=3.6e-12  Score=58.73  Aligned_cols=42  Identities=19%  Similarity=0.311  Sum_probs=35.6

Q ss_pred             EEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          16 LKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        16 l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |||+|||.++++++|+++|+++| +..+.      .++++|||||+|.+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~------~~~~~g~afv~f~~   42 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCF------VDKYKGTAFVTLLN   42 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEE------EETTTTEEEEEESS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-cccee------ecccceeEEEEECC
Confidence            79999999999999999999998 44443      34578999999976

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=1.2e-11  Score=59.89  Aligned_cols=47  Identities=28%  Similarity=0.508  Sum_probs=40.0

Q ss_pred             CCcEEEEe--cCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          12 GMVSLKVD--NLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        12 ~~~~l~v~--~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      ...+++|.  |||..+++++|+++|++||.|..+.+..+      +|||||+|.+
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~   65 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRT   65 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESS
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECC
Confidence            34778885  59999999999999999999999876543      5899999976

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.04  E-value=8.4e-11  Score=57.07  Aligned_cols=48  Identities=8%  Similarity=-0.052  Sum_probs=39.2

Q ss_pred             CCcEEEEecCCCCC-CH----HHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEeeC
Q psy7053          12 GMVSLKVDNLTYRT-TP----DDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLLF   65 (65)
Q Consensus        12 ~~~~l~v~~l~~~~-~~----~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~~   65 (65)
                      ...+|||+||+.++ ++    +.|+.+|+.||.|..+.+..      .+++|||+|.+.
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~   56 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNP   56 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSST
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCH
Confidence            45789999999875 32    56899999999999987753      578999999863

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.99  E-value=1.1e-11  Score=60.20  Aligned_cols=49  Identities=12%  Similarity=0.200  Sum_probs=42.1

Q ss_pred             EEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          15 SLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        15 ~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+++.+++..+.++.++++|++||.|.++.++.+ .+++++|+|||+|.+
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~   77 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRR   77 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEec
Confidence            4666677777788899999999999999998766 589999999999975

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.91  E-value=1.4e-09  Score=50.54  Aligned_cols=45  Identities=11%  Similarity=0.105  Sum_probs=37.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      .+.|+|+++|++.+++.|+ .|+++|.|.++.+.      ..+||+||+|.+
T Consensus         4 ~~wV~V~G~p~~~~~~il~-~F~~~G~I~~~~~~------~~~~~~fV~f~~   48 (81)
T d1wwha1           4 DTWVTVFGFPQASASYILL-QFAQYGNILKHVMS------NTGNWMHIRYQS   48 (81)
T ss_dssp             GGEEEEECCCGGGHHHHHH-HHHTTSCEEEEEEC------SSSSEEEEEESS
T ss_pred             ccEEEEECCChHHHHHHHH-HHHhhhhhheEEec------CCCCEEEEEEcc
Confidence            4689999999998876665 69999999988653      357999999986

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.63  E-value=3.7e-08  Score=47.06  Aligned_cols=54  Identities=19%  Similarity=0.291  Sum_probs=41.2

Q ss_pred             CCCCCCCcEEEEecC--CCCCC---------HHHHHHHhhccCCEEEEEEeecCCCCCcccEEEEEEee
Q psy7053           7 PPRIEGMVSLKVDNL--TYRTT---------PDDLRRVFERCGEVGDIYIPRDRFTRESRGFAFVRLLL   64 (65)
Q Consensus         7 ~~~~~~~~~l~v~~l--~~~~~---------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~~fv~f~~   64 (65)
                      |.....+++|++.|+  |.+..         .+++++.|+.+|.|..+.+..+    ..+|++||+|.+
T Consensus         2 p~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~   66 (99)
T d2dita1           2 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRD   66 (99)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSC
T ss_pred             CCCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECC
Confidence            455667799999998  54321         2578899999999998876443    467999999976

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.37  E-value=2.7e-07  Score=44.25  Aligned_cols=52  Identities=25%  Similarity=0.215  Sum_probs=39.7

Q ss_pred             CcEEEEecC--CCCCC--------HHHHHHHhhccCCEEEEEEeecCCC--CCcccEEEEEEee
Q psy7053          13 MVSLKVDNL--TYRTT--------PDDLRRVFERCGEVGDIYIPRDRFT--RESRGFAFVRLLL   64 (65)
Q Consensus        13 ~~~l~v~~l--~~~~~--------~~~l~~~f~~~g~i~~~~~~~~~~~--~~~~g~~fv~f~~   64 (65)
                      ++.|.+.|+  +....        .+++++.|.++|.|.++.++.++.+  ....|++||+|.+
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~   67 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTS   67 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESC
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECC
Confidence            478999998  44432        2468889999999999998876544  3346899999986

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.47  E-value=0.01  Score=27.42  Aligned_cols=51  Identities=10%  Similarity=0.055  Sum_probs=38.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhccCCEEEEEEeecCCCCCcc--cEEEEEEee
Q psy7053          14 VSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPRDRFTRESR--GFAFVRLLL   64 (65)
Q Consensus        14 ~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~--g~~fv~f~~   64 (65)
                      .+|-|..||...+++++.+.+...+.+.....+....+.+..  .-|||.|.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~   54 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKN   54 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESS
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCC
Confidence            578999999999999999999999988877666554343322  567888754

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.88  E-value=0.69  Score=21.44  Aligned_cols=34  Identities=15%  Similarity=0.130  Sum_probs=27.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhccCCEEEEEEee
Q psy7053          13 MVSLKVDNLTYRTTPDDLRRVFERCGEVGDIYIPR   47 (65)
Q Consensus        13 ~~~l~v~~l~~~~~~~~l~~~f~~~g~i~~~~~~~   47 (65)
                      ...||.-..|......+|.++|++||.| .+.++-
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V-~VswId   48 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWID   48 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEE
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCce-EEEEec
Confidence            3569999999999999999999999976 333443